3WDS | pdb_00003wds

Crystal structure of 3-quinuclidinone reductase from Agrobacterium tumefaciens

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.183 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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

Literature

Structural basis for high substrate-binding affinity of 3-quinuclidinone reductase AtQR

Hou, F., Miyakawa, T., Kataoka, M., Takeshita, D., Kumashiro, S., Nagata, K., Shimizu, S., Tanokura, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 112.65 kDa 
  • Atom Count: 8,271 
  • Modeled Residue Count: 1,028 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH-dependent quinuclidinone reductaseA,
B,
C [auth D],
D [auth C]		263Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for G1K3P5 (Agrobacterium tumefaciens)
Explore G1K3P5 
Go to UniProtKB:  G1K3P5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1K3P5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD


Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY

Query on ACY


Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
J [auth D],
L [auth C]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.183 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.97α = 90
b = 126.37β = 110.5
c = 62.02γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description