3F1L | pdb_00003f1l

The 0.95 A structure of an oxidoreductase, yciK from E.coli

PDB DOI: https://doi.org/10.2210/pdb3F1L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-28 Released: 2008-11-18
Deposition Author(s): Vijayalakshmi, J., Woodard, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free:
0.192 (Depositor), 0.186 (DCC)
R-Value Work:
0.171 (Depositor), 0.166 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure of an oxidoreductase, yciK from E. coli, in two crystal forms - NADP+ unbound structure at 0.95 A resolution

Vijayalakshmi, J., Meredith, T.C., Woodard, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 55.92 kDa
Atom Count: 4,603
Modeled Residue Count: 489
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase yciK	A, B	252	Escherichia coli K-12	Mutation(s): 0 Gene Names: b1271, JW1263, yciK EC: 1
UniProt
Find proteins for P31808 (Escherichia coli (strain K12)) Explore P31808 Go to UniProtKB: P31808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31808
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free: 0.192 (Depositor), 0.186 (DCC)
R-Value Work: 0.171 (Depositor), 0.166 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.871	α = 90
b = 66.803	β = 109.03
c = 65.053	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Vijayalakshmi, J.

Revision History (Full details and data files)

Version 1.0: 2008-11-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Refinement description

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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.