4BFL | pdb_00004bfl

Structure of natively expressed catalase HPII

PDB DOI: https://doi.org/10.2210/pdb4BFL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-19 Released: 2013-04-03
Deposition Author(s): Gabrielsen, M., Schuttelkopf, A.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.202 (Depositor), 0.216 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.176 (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

Accidents Happen: Crystallisation of Catalase from a Mixed Protein Solution

Gabrielsen, M., Schuttelkopf, A.W., Akpunarlieva, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 339.74 kDa
Atom Count: 25,648
Modeled Residue Count: 2,967
Deposited Residue Count: 3,012
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE HPII	A, B, C, D	753	Escherichia coli BL21(DE3)	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for P21179 (Escherichia coli (strain K12)) Explore P21179 Go to UniProtKB: P21179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], F [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 F [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain K [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	G [auth B], H [auth B], J [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.202 (Depositor), 0.216 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.402	α = 90
b = 171.669	β = 104.67
c = 123.209	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Gabrielsen, M.

Schuttelkopf, A.W.

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2013-04-17
Changes: Atomic model
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

4BFL | pdb_00004bfl

Structure of natively expressed catalase HPII

Literature

Accidents Happen: Crystallisation of Catalase from a Mixed Protein Solution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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