2DPH | pdb_00002dph

Crystal Structure of Formaldehyde dismutase

PDB DOI: https://doi.org/10.2210/pdb2DPH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Mutation(s): No

Deposited: 2006-05-11 Released: 2007-05-29
Deposition Author(s): Hasegawa, T., Yamano, A., Yanase, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The X-ray crystal structure of formaldehyde dismutase at 2.3 A resolution

Hasegawa, T., Yamano, A., Miura, K., Katsube, Y., Yanase, H., Kato, N.

(2002) Acta Crystallogr A 58: C102-C102

Macromolecule Content

Total Structure Weight: 87.39 kDa
Atom Count: 6,374
Modeled Residue Count: 796
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formaldehyde dismutase	A, B	398	Pseudomonas putida	Mutation(s): 0 EC: 1.2.99.4 (PDB Primary Data), 1.2.98.1 (UniProt)
UniProt
Find proteins for Q52078 (Pseudomonas putida) Explore Q52078 Go to UniProtKB: Q52078
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52078
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.229	α = 90
b = 90.229	β = 90
c = 226.689	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Hasegawa, T.

Yamano, A.

Yanase, H.

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

2DPH | pdb_00002dph

Crystal Structure of Formaldehyde dismutase

Literature

The X-ray crystal structure of formaldehyde dismutase at 2.3 A resolution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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