3F5Q | pdb_00003f5q

CRYSTAL STRUCTURE OF putative short chain dehydrogenase from Escherichia coli CFT073

PDB DOI: https://doi.org/10.2210/pdb3F5Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli O6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-04 Released: 2009-01-13
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.215 (Depositor), 0.226 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3F5Q

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of an uncharacterized protein

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 58.36 kDa
Atom Count: 3,959
Modeled Residue Count: 457
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dehydrogenase	A, B	262	Escherichia coli O6	Mutation(s): 0 Gene Names: AAN80202.1, c1736, yciK EC: 1
UniProt
Find proteins for A0A0H2V6Y9 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V6Y9 Go to UniProtKB: A0A0H2V6Y9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2V6Y9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.215 (Depositor), 0.226 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.412	α = 100.29
b = 48.011	β = 102.67
c = 65.232	γ = 105.26

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Structure summary
Version 1.5: 2023-12-27
Changes: Data collection, Database references

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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.