3WDS

Crystal structure of 3-quinuclidinone reductase from Agrobacterium tumefaciens

PDB DOI: https://doi.org/10.2210/pdb3WDS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Agrobacterium tumefaciens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-22 Released: 2014-06-25
Deposition Author(s): Hou, F., Miyakawa, T., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 1,028
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent quinuclidinone reductase	A, B, C [auth D], D [auth C]	263	Agrobacterium tumefaciens	Mutation(s): 0
UniProt
Find proteins for G1K3P5 (Rhizobium radiobacter) Explore G1K3P5 Go to UniProtKB: G1K3P5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G1K3P5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth D] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth D] mmCIF format, chain L [auth C]	F [auth A], I [auth B], J [auth D], L [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth D] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth D] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.150 (Depositor), 0.160 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.97	α = 90
b = 126.37	β = 110.5
c = 62.02	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Hou, F.

Miyakawa, T.

Tanokura, M.

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