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

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

View more in-depth experimental data

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

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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.