3SLH | pdb_00003slh

1.70 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii in complex with shikimate-3-phosphate and glyphosate

PDB DOI: https://doi.org/10.2210/pdb3SLH/pdb

Classification: TRANSFERASE
Organism(s): Coxiella burnetii RSA 493
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-24 Released: 2011-07-20
Deposition Author(s): Light, S.H., Minasov, G., Filippova, E.V., Krishna, S.N., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.182 (Depositor), 0.190 (DCC)
R-Value Work:
0.149 (Depositor), 0.160 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

1.70 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase(AroA) from Coxiella burnetii in complex with shikimate-3-phosphate and glyphosate

Light, S.H., Minasov, G., Filippova, E.V., Krishna, S.N., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 193.13 kDa
Atom Count: 15,366
Modelled Residue Count: 1,753
Deposited Residue Count: 1,764
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoshikimate 1-carboxyvinyltransferase	A, B, C, D	441	Coxiella burnetii RSA 493	Mutation(s): 0 Gene Names: aroA, CBU_0526 EC: 2.5.1.19
UniProt
Find proteins for Q83E11 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore Q83E11 Go to UniProtKB: Q83E11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q83E11
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S3P Query on S3P Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain TA [auth D] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain V [auth B]	I [auth A], JA [auth C], TA [auth D], V [auth B]	SHIKIMATE-3-PHOSPHATE C₇ H₁₁ O₈ P QYOJSKGCWNAKGW-PBXRRBTRSA-N		Interactions Focus chain I [auth A] Focus chain JA [auth C] Focus chain TA [auth D] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain JA [auth C] Focus chain TA [auth D] Focus chain V [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain DA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain DA [auth B]	DA [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Interactions & Density Focus chain DA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain PA [auth C] SDF format, chain YA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain YA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain YA [auth D]	LA [auth C], PA [auth C], YA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain LA [auth C] Focus chain PA [auth C] Focus chain YA [auth D] Interactions & Density Focus chain LA [auth C] Focus chain PA [auth C] Focus chain YA [auth D]
SKM Query on SKM Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain UA [auth D] SDF format, chain X [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain X [auth B]	IA [auth C], K [auth A], UA [auth D], X [auth B]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₇ H₁₀ O₅ JXOHGGNKMLTUBP-HSUXUTPPSA-N		Interactions Focus chain IA [auth C] Focus chain K [auth A] Focus chain UA [auth D] Focus chain X [auth B] Interactions & Density Focus chain IA [auth C] Focus chain K [auth A] Focus chain UA [auth D] Focus chain X [auth B]
GPJ Query on GPJ Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain SA [auth D] SDF format, chain W [auth B] SDF format, chain Y [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B]	HA [auth C], J [auth A], SA [auth D], W [auth B], Y [auth B]	GLYPHOSATE C₃ H₉ N O₅ P XDDAORKBJWWYJS-UHFFFAOYSA-O		Interactions Focus chain HA [auth C] Focus chain J [auth A] Focus chain SA [auth D] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth C] Focus chain J [auth A] Focus chain SA [auth D] Focus chain W [auth B] Focus chain Y [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain Z [auth B]	AA [auth B] CA [auth B] KA [auth C] M [auth A] MA [auth C] AA [auth B], CA [auth B], KA [auth C], M [auth A], MA [auth C], N [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], VA [auth D], WA [auth D], XA [auth D], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain KA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain KA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Z [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain U [auth B]	G [auth A], GA [auth C], H [auth A], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain U [auth B]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain QA [auth D] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain T [auth B]	E [auth A], EA [auth C], F [auth A], QA [auth D], T [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain QA [auth D] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain QA [auth D] Focus chain T [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C]	L [auth A], NA [auth C], O [auth A], OA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Interactions & Density Focus chain L [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain RA [auth D] MOL2 format, chain FA [auth C] MOL2 format, chain RA [auth D] mmCIF format, chain FA [auth C] mmCIF format, chain RA [auth D]	FA [auth C], RA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain RA [auth D] Interactions & Density Focus chain FA [auth C] Focus chain RA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.182 (Depositor), 0.190 (DCC)
R-Value Work: 0.149 (Depositor), 0.160 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33slh

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.252	α = 90
b = 186.638	β = 91.51
c = 95.794	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description