3H7A | pdb_00003h7a

CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb3H7A/pdb

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

Deposited: 2009-04-24 Released: 2009-05-05
Deposition Author(s): Patskovsky, Y., Toro, R., Morano, C., Freeman, J., Miller, 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: 1.87 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.205 (Depositor), 0.209 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris

Patskovsky, Y., Toro, R., Morano, C., Miller, S., Freeman, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 109.69 kDa
Atom Count: 6,980
Modeled Residue Count: 849
Deposited Residue Count: 1,008
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	252	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0021
UniProt
Find proteins for Q6NDT3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NDT3 Go to UniProtKB: Q6NDT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NDT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth C], F [auth D], G [auth D]	Unknown ligand		Interactions Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.241 (Depositor), 0.247 (DCC)
R-Value Work: 0.205 (Depositor), 0.209 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.431	α = 90
b = 91.431	β = 90
c = 270.709	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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