3QAN | pdb_00003qan

Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from bacillus halodurans

PDB DOI: https://doi.org/10.2210/pdb3QAN/pdb

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

Deposited: 2011-01-11 Released: 2011-02-02
Deposition Author(s): Patskovsky, Y., Toro, R., Foti, R., Seidel, R.D., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

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

Literature

Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase from Bacillus Halodurans

Patskovsky, Y., Toro, R., Foti, R., Seidel, R.D., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 178.96 kDa
Atom Count: 12,781
Modeled Residue Count: 1,547
Deposited Residue Count: 1,614
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-pyrroline-5-carboxylate dehydrogenase 1	A, B, C	538	Halalkalibacterium halodurans	Mutation(s): 0 Gene Names: rocA1, BH2737 EC: 1.5.1.12 (PDB Primary Data), 1.2.1.88 (UniProt)
UniProt
Find proteins for Q9K9B2 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9K9B2 Go to UniProtKB: Q9K9B2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K9B2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.897	α = 90
b = 75.559	β = 98.48
c = 217.39	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.