3ADP | pdb_00003adp

Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase (NADH Form)

PDB DOI: https://doi.org/10.2210/pdb3ADP/pdb
Entry: 3ADP supersedes: 3A97

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

Deposited: 2010-01-26 Released: 2010-02-09
Deposition Author(s): Asada, Y., Hara, A., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase

Asada, Y., Hara, A., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 35.91 kDa
Atom Count: 2,889
Modeled Residue Count: 310
Deposited Residue Count: 319
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lambda-crystallin	A	319	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: CRYL1, GUL3DH EC: 1.1.1.45
UniProt
Find proteins for P14755 (Oryctolagus cuniculus) Explore P14755 Go to UniProtKB: P14755
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14755
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.016	α = 90
b = 69.517	β = 102.7
c = 65.096	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 3A97

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
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.