4CVM

PaMurF in complex with AMP-PNP and UDP-MurNAc-tripeptide (mDAP)

• PDB DOI: https://doi.org/10.2210/pdb4CVM/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-28 Released: 2015-04-22 
• Deposition Author(s): Ruane, K.M., Majce, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Pamurf in Complex with AMP-Pnp and Udp-Murnac-Tripeptide

Majce, V., Ruane, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.85 kDa 
• Atom Count: 3,305 
• Modelled Residue Count: 443 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE	A	475	Pseudomonas aeruginosa PAO1	Mutation(s): 0  EC: 6.3.2.10
UniProt
Find proteins for Q9HVZ7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVZ7  Go to UniProtKB:  Q9HVZ7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	F [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UDP	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MUB	D [auth A]	N-acetyl-alpha-muramic acid C11 H19 N O8 MNLRQHMNZILYPY-MDMHTWEWSA-N
FGA	E [auth A]	GAMMA-D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N
ALA	B [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
MG	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.224 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.54	α = 90
b = 86.05	β = 90
c = 88.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Ruane, K.M., Majce, V.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Structure summary