4LFG

Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, fully liganded complex;

PDB DOI: https://doi.org/10.2210/pdb4LFG/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus uberis 0140J
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-26 Released: 2013-07-10
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.184
R-Value Work: 0.153
R-Value Observed: 0.154

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

Crystal Structure of Geranylgeranyl Diphosphate Synthase from Streptococcus Uberis 0140J

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 65.73 kDa
Atom Count: 5,227
Modelled Residue Count: 578
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl Diphosphate Synthase	A, B	290	Streptococcus uberis 0140J	Mutation(s): 0 Gene Names: fps, SUB1274 EC: 2.5.1.10
UniProt
Find proteins for B9DUT7 (Streptococcus uberis (strain ATCC BAA-854 / 0140J)) Explore B9DUT7 Go to UniProtKB: B9DUT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9DUT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPE Query on IPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C₅ H₁₂ O₇ P₂ NUHSROFQTUXZQQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.184
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.385	α = 90
b = 74.326	β = 90
c = 124.473	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description