4G4Y

Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb4G4Y/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-16 Released: 2013-07-24
Deposition Author(s): Lee, W.C., Song, J.H., Park, J.S., Kim, H.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.224
R-Value Work: 0.197

wwPDB Validation 3D Report Full Report

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

Literature

Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA

Lee, W.C., Park, J.S., Song, J.H., Kim, S.I., Lee, J.C., Cheong, J., Kim, H.Y.

To be published.

Macromolecule Content

Total Structure Weight: 112.52 kDa
Atom Count: 8,751
Modelled Residue Count: 970
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein Omp38	A, B, C, D, E A, B, C, D, E, F, G, H	123	Acinetobacter baumannii	Mutation(s): 0 Gene Names: omp38, ompA
UniProt
Find proteins for Q6RYW5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore Q6RYW5 Go to UniProtKB: Q6RYW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6RYW5
Sequence Annotations Expand
Reference Sequence

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 J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.224
R-Value Work: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.09	α = 90
b = 98.49	β = 105.9
c = 98.06	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Help and Resources

4G4Y

Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)