4G4W | pdb_00004g4w

Crystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb4G4W/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Acinetobacter baumannii TCDC-AB0715
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: 1.90 Å
R-Value Free:
0.229 (Depositor), 0.209 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)

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: 13.19 kDa
Atom Count: 959
Modeled Residue Count: 108
Deposited Residue Count: 114
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan-associated lipoprotein	A	114	Acinetobacter baumannii TCDC-AB0715	Mutation(s): 0 Gene Names: ABTW07_3009, pal

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229 (Depositor), 0.209 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.14	α = 90
b = 54.14	β = 90
c = 114.03	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

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 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations