6UUK

Crystal structure of muramoyltetrapeptide carboxypeptidase from Oxalobacter formigenes

• PDB DOI: https://doi.org/10.2210/pdb6UUK/pdb

• Classification: HYDROLASE
• Organism(s): Oxalobacter formigenes OXCC13
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-30 Released: 2020-11-04 
• Deposition Author(s): Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.229 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Crystal structure of muramoyltetrapeptide carboxypeptidase from Oxalobacter formigenes

Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content

• Total Structure Weight: 78.83 kDa 
• Atom Count: 4,486 
• Modelled Residue Count: 576 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muramoyltetrapeptide carboxypeptidase	A, B	349	Oxalobacter formigenes OXCC13	Mutation(s): 0  Gene Names: idcA, OFBG_01115 EC: 3.4.17.13
UniProt
Find proteins for C3XA61 (Oxalobacter formigenes OXCC13) Explore C3XA61  Go to UniProtKB:  C3XA61

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.229 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: P 6₃
• Diffraction Data: https://doi.org/10.18430/m36uuk

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.443	α = 90
b = 82.443	β = 90
c = 149.293	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Chang, C., Tesar, C., Endres, M., Babnigg, G., Hassan, H., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary