6LFK | pdb_00006lfk

Crystal structure of KatE from atypical E. coli

PDB DOI: https://doi.org/10.2210/pdb6LFK/pdb
Entry: 6LFK supersedes: 6JOA

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

Deposited: 2019-12-03 Released: 2020-12-09
Deposition Author(s): Cho, H.S., Yoo, Y., Park, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.223 (Depositor), 0.221 (DCC)
R-Value Work:
0.188 (Depositor), 0.187 (DCC)

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

Crystal structure of eKatE

Cho, H.S., Yoo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 340.25 kDa
Atom Count: 23,791
Modeled Residue Count: 2,883
Deposited Residue Count: 3,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eKatE catalase	A, B, C, D	750	Escherichia coli	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for A0A6I8WFM0 (Escherichia coli M8) Explore A0A6I8WFM0 Go to UniProtKB: A0A6I8WFM0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6I8WFM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [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 G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223 (Depositor), 0.221 (DCC)
R-Value Work: 0.188 (Depositor), 0.187 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.585	α = 90
b = 178.935	β = 106.699
c = 107.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Cho, H.S.

Yoo, Y.

Park, J.B.

This entry supersedes: 6JOA

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2021-04-21
Changes: Advisory
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

6LFK | pdb_00006lfk

Crystal structure of KatE from atypical E. coli

Literature

Crystal structure of eKatE

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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