4S12 | pdb_00004s12

1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.

• PDB DOI: https://doi.org/10.2210/pdb4S12/pdb

• Classification: LYASE
• Organism(s): Yersinia enterocolitica subsp. palearctica Y11
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-07 Released: 2015-01-21 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.170 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from Yersinia enterocolitica.

Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.07 kDa 
• Atom Count: 8,159 
• Modeled Residue Count: 870 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramic acid 6-phosphate etherase	A, B, C	298	Yersinia enterocolitica subsp. palearctica Y11	Mutation(s): 0  Gene Names: murQ, Y11_42431 EC: 4.2.1.126
UniProt
Find proteins for A0A0H2UKZ5 (Yersinia enterocolitica subsp. palearctica serotype O:3 (strain DSM 13030 / CIP 106945 / Y11)) Explore A0A0H2UKZ5  Go to UniProtKB:  A0A0H2UKZ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	M [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.170 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34s12

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.287	α = 90
b = 81.734	β = 103.21
c = 58.848	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description