6UUK | pdb_00006uuk

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.229 (Depositor), 0.226 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6UUK

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C3XA61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.226 (DCC)
R-Value Work: 0.204 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Diffraction Data:

Space Group: P 6₃

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-11-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.