3IG4 | pdb_00003ig4

Structure of a putative aminopeptidase P from Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb3IG4/pdb

Classification: HYDROLASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-27 Released: 2009-08-04
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Skarina, T., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.226 (Depositor), 0.216 (DCC)
R-Value Work:
0.198 (Depositor), 0.193 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of a putative aminopeptidase P from Bacillus anthracis

Anderson, S.M., Wawrzak, Z., Skarina, T., Onopriyenko, O., Kwon, K., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 300.44 kDa
Atom Count: 20,528
Modelled Residue Count: 2,514
Deposited Residue Count: 2,562
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-pro aminopeptidase	A, B, C, D, E A, B, C, D, E, F	427	Bacillus anthracis	Mutation(s): 0 Gene Names: BAS1763, BA_1901, GBAA1901, GBAA_1901 EC: 3.4.11.9
UniProt
Find proteins for A0A6L8PS06 (Bacillus anthracis) Explore A0A6L8PS06 Go to UniProtKB: A0A6L8PS06
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8PS06
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F]	AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth C], AB [auth F], BA [auth C], BB [auth F], CA [auth C], CB [auth F], DA [auth C], DB [auth F], EA [auth C], FA [auth C], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], X [auth B], YA [auth F], ZA [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain X [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	G [auth A] GA [auth D] H [auth A] HA [auth D] PA [auth E] G [auth A], GA [auth D], H [auth A], HA [auth D], PA [auth E], Q [auth B], QA [auth E], R [auth B], WA [auth F], XA [auth F], Y [auth C], Z [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain Z [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.226 (Depositor), 0.216 (DCC)
R-Value Work: 0.198 (Depositor), 0.193 (DCC)
R-Value Observed: 0.199 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33ig4

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.88	α = 90
b = 180.88	β = 90
c = 254.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-12-14
Changes: Database references, Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary