4G88 | pdb_00004g88

Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb4G88/pdb

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

Deposited: 2012-07-22 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:
0.234 (Depositor), 0.211 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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: 112.86 kDa
Atom Count: 8,558
Modeled Residue Count: 973
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6RYW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
API Query on API Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain P [auth G] SDF format, chain R [auth H] SDF format, chain O [auth F] SDF format, chain K [auth C] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain P [auth G] MOL2 format, chain R [auth H] MOL2 format, chain O [auth F] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain P [auth G] mmCIF format, chain R [auth H] mmCIF format, chain O [auth F] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B]	I [auth A] J [auth B] K [auth C] L [auth D] N [auth E] I [auth A], J [auth B], K [auth C], L [auth D], N [auth E], O [auth F], P [auth G], R [auth H]	2,6-DIAMINOPIMELIC ACID C₇ H₁₄ N₂ O₄ GMKMEZVLHJARHF-SYDPRGILSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain R [auth H]
SRT Query on SRT Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain Q [auth G] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth G] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth G]	M [auth D], Q [auth G]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain M [auth D] Focus chain Q [auth G] Interactions & Density Focus chain M [auth D] Focus chain Q [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.234 (Depositor), 0.211 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.52	α = 90
b = 99.3	β = 105.95
c = 98.12	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations

4G88 | pdb_00004g88

Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand