3T37 | pdb_00003t37

Crystal structure of pyridoxine 4-oxidase from Mesorbium loti

PDB DOI: https://doi.org/10.2210/pdb3T37/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mesorhizobium loti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-25 Released: 2012-08-15
Deposition Author(s): Mugo, A.N., Kobayashi, J., Mikami, B., Ohnishi, K., Yagi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.220 (Depositor), 0.214 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure biology and crystallization communication

Mugo, A.N., Kobayashi, J., Mikami, B., Ohnishi, K., Yagi, T.

To be published.

Macromolecule Content

Total Structure Weight: 57.4 kDa
Atom Count: 4,140
Modeled Residue Count: 509
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable dehydrogenase	A	526	Mesorhizobium loti	Mutation(s): 0 Gene Names: mll6785, pno EC: 1.1.3.12
UniProt
Find proteins for Q5NT46 (Rhizobium loti) Explore Q5NT46 Go to UniProtKB: Q5NT46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NT46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.220 (Depositor), 0.214 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 79.438	β = 90
c = 136.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2018-01-24
Changes: Data collection, Experimental preparation
Version 1.2: 2019-03-13
Changes: Data collection
Version 1.3: 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.