3VLM | pdb_00003vlm

Crystal Structure Analysis of the Met244Ala Variant of KatG from Haloarcula marismortui

PDB DOI: https://doi.org/10.2210/pdb3VLM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Haloarcula marismortui ATCC 43049
Expression System: Haloferax volcanii
Mutation(s): Yes

Deposited: 2011-12-01 Released: 2012-12-05
Deposition Author(s): Sato, T., Ten-i, T., Higuchi, W., Yoshimatsu, K., Fujiwara, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.325 (Depositor), 0.308 (DCC)
R-Value Work:
0.283 (Depositor), 0.267 (DCC)
R-Value Observed:
0.285 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure and Kinetic Studies on Met244Ala Variant of KatG from HALOARCULA MARISMORTUI

Sato, T., Ten-i, T., Higuchi, W., Yoshimatsu, K., Fujiwara, T.

To be published.

Macromolecule Content

Total Structure Weight: 165.69 kDa
Atom Count: 10,623
Modeled Residue Count: 1,323
Deposited Residue Count: 1,474
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase 2	A, B	737	Haloarcula marismortui ATCC 43049	Mutation(s): 1 Gene Names: katG2 EC: 1.11.1.21
UniProt
Find proteins for O59651 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore O59651 Go to UniProtKB: O59651
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.325 (Depositor), 0.308 (DCC)
R-Value Work: 0.283 (Depositor), 0.267 (DCC)
R-Value Observed: 0.285 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 315.83	α = 90
b = 81.05	β = 100.04
c = 74.84	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
REFMAC	refinement
CrystalClear	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.