7TI7 | pdb_00007ti7

Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb7TI7/pdb

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


• Deposited: 2022-01-12 Released: 2022-01-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW in complex with ADP

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.77 kDa 
• Atom Count: 3,947 
• Modelled Residue Count: 442 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoylalanine--D-glutamate ligase	A	456	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  murD, Aba9201_12330, ABUW_3630, APC21_11165, C6N18_02095, EA686_02860, EGM95_19310, F2P40_16560, GNY86_17350, NCTC13421_03598, SI89_12870 EC: 6.3.2.9
UniProt
Find proteins for B7H1N2 (Acinetobacter baumannii (strain AB307-0294)) Explore B7H1N2  Go to UniProtKB:  B7H1N2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	D [auth A], E [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37TI7

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.49	α = 90
b = 91.82	β = 90
c = 106.36	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection