3EDM | pdb_00003edm

Crystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens

PDB DOI: https://doi.org/10.2210/pdb3EDM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-03 Released: 2008-09-30
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Chang, S., Romero, R., Wasserman, S., 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: 2.30 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens

Bonanno, J.B., Rutter, M., Bain, K.T., Chang, S., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 107.65 kDa
Atom Count: 6,462
Modeled Residue Count: 880
Deposited Residue Count: 1,036
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D	259	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: AGR_L_3556, Atu3026
UniProt
Find proteins for A9CEK0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEK0 Go to UniProtKB: A9CEK0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CEK0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.501	α = 90
b = 131.26	β = 90
c = 67.952	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, 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: 2024-02-21
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.