4CVK | pdb_00004cvk

PaMurF in complex with UDP-MurNAc-tripeptide (mDAP)

• PDB DOI: https://doi.org/10.2210/pdb4CVK/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
• 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: 1.92 Å
• R-Value Free: 
  0.226 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Pamurf in Complex with Udp-Murnac-Tripeptide (Mdap)

Majce, V., Ruane, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,298 
• Modeled Residue Count: 441 
• Deposited Residue Count: 478 
• Unique protein chains: 2

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  Gene Names: murF 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-FGA-API	B	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.226 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.81	α = 90
b = 87.29	β = 90
c = 92.61	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: 2015-04-29
  Changes: Structure summary
• Version 1.2: 2015-09-23
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 2.0: 2022-12-07
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.1: 2024-01-31
  Changes: Refinement description