3CAN | pdb_00003can

Crystal structure of a domain of pyruvate-formate lyase-activating enzyme from Bacteroides vulgatus ATCC 8482

PDB DOI: https://doi.org/10.2210/pdb3CAN/pdb

Classification: LYASE ACTIVATOR
Organism(s): Phocaeicola vulgatus ATCC 8482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-20 Released: 2008-03-04
Deposition Author(s): Nocek, B., Hendricks, R., Hatzos, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.182 (Depositor), 0.183 (DCC)
R-Value Work:
0.162 (Depositor), 0.166 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a domain of pyruvate-formate lyase-activating enzyme from Bacteroides vulgatus ATCC 8482.

Nocek, B., Hendricks, R., Hatzos, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.44 kDa
Atom Count: 1,476
Modeled Residue Count: 161
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate-formate lyase-activating enzyme	A	182	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: BVU_1420 EC: 1.97.1.4
UniProt
Find proteins for A6L094 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L094 Go to UniProtKB: A6L094
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6L094
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.182 (Depositor), 0.183 (DCC)
R-Value Work: 0.162 (Depositor), 0.166 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.768	α = 90
b = 73.768	β = 90
c = 101.358	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
PHENIX	phasing
REFMAC	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-04

Deposition Author(s):

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-03-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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.