7SIR

Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW

PDB DOI: https://doi.org/10.2210/pdb7SIR/pdb

Classification: LIGASE
Organism(s): Acinetobacter baumannii AB307-0294
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-14 Released: 2021-11-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.192
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 49.11 kDa
Atom Count: 3,655
Modelled Residue Count: 431
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoylalanine--D-glutamate ligase	A	456	Acinetobacter baumannii AB307-0294	Mutation(s): 0 Gene Names: murD, ABBFA_003287 EC: 6.3.2.9
UniProt
Find proteins for B7H1N2 (Acinetobacter baumannii (strain AB307-0294)) Explore B7H1N2 Go to UniProtKB: B7H1N2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7H1N2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.192
R-Value Work: 0.168
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M37SIR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.17	α = 90
b = 86.24	β = 90
c = 94.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History (Full details and data files)

Version 1.0: 2021-11-03
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.