4G4V | pdb_00004g4v

Crystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb4G4V/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:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.226 (Depositor), 0.226 (DCC)

Starting Model: experimental
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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: 13 kDa
Atom Count: 943
Modeled Residue Count: 111
Deposited Residue Count: 114
Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
API Query on API 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]	2,6-DIAMINOPIMELIC ACID C₇ H₁₄ N₂ O₄ GMKMEZVLHJARHF-SYDPRGILSA-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: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.226 (Depositor), 0.226 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.04	α = 90
b = 45.13	β = 90
c = 50.07	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.