6PO0 | pdb_00006po0

The structure of the orthorhombic (P212121) crystal form of beef liver catalase at 1.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb6PO0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Expression System: Bos taurus
Mutation(s): Yes

Deposited: 2019-07-03 Released: 2020-05-20
Deposition Author(s): McPherson, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.207 (Depositor), 0.208 (DCC)
R-Value Work:
0.173 (Depositor), 0.178 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution

McPherson, A.

To be published.

Macromolecule Content

Total Structure Weight: 245.45 kDa
Atom Count: 17,727
Modeled Residue Count: 1,996
Deposited Residue Count: 2,108
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	527	Bos taurus	Mutation(s): 2 Gene Names: CAT EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus) Explore P00432 Go to UniProtKB: P00432
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	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] Interactions & Density 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 K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B]	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] Interactions & Density 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: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.207 (Depositor), 0.208 (DCC)
R-Value Work: 0.173 (Depositor), 0.178 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.984	α = 90
b = 140.386	β = 90
c = 228.177	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

McPherson, A.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Refinement description

6PO0 | pdb_00006po0

The structure of the orthorhombic (P212121) crystal form of beef liver catalase at 1.85 A resolution

Literature

The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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