5GKN

Catalase structure determined by electron crystallography of thin 3D crystals

PDB DOI: https://doi.org/10.2210/pdb5GKN/pdb
Entry: 5GKN supersedes: 3J7U

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2016-07-04 Released: 2016-10-26
Deposition Author(s): Yonekura, K.

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 3.20 Å
R-Value Free: 0.304
R-Value Work: 0.251
R-Value Observed: 0.252

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Refinement of Cryo-EM Structures Using Scattering Factors of Charged Atoms

Yonekura, K., Maki-Yonekura, M.

(2016) J Appl Crystallogr 49: 1517-1523

DOI: https://doi.org/10.1107/S1600576716011274

Macromolecule Content

Total Structure Weight: 245.44 kDa
Atom Count: 16,548
Modelled Residue Count: 1,996
Deposited Residue Count: 2,108
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	527	Bos taurus	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus) Explore P00432 Go to UniProtKB: P00432
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00432
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 3.20 Å
R-Value Free: 0.304
R-Value Work: 0.251
R-Value Observed: 0.252
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69	α = 90
b = 173.5	β = 90
c = 206	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
EDINT	data scaling
Modified version of phenix	phasing
Modified	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Yonekura, K.

This entry supersedes: 3J7U

Funding Organization	Location	Grant Number
	Japan	--

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5GKN

Catalase structure determined by electron crystallography of thin 3D crystals

Refinement of Cryo-EM Structures Using Scattering Factors of Charged Atoms

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)