5XZM

CATPO mutant - V228I

PDB DOI: https://doi.org/10.2210/pdb5XZM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycothermus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-07-12 Released: 2018-07-18
Deposition Author(s): Yuzugullu Karakus, Y., Balci, S., Goc, G., Pearson, A.R., Yorke, B.
Funding Organization(s): TUBITAK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

CATPO mutant - V228I

Yuzugullu Karakus, Y., Balci, S., Goc, G., Pearson, A.R., Yorke, B.

To be published.

Macromolecule Content

Total Structure Weight: 303.24 kDa
Atom Count: 24,285
Modelled Residue Count: 2,699
Deposited Residue Count: 2,712
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	678	Mycothermus thermophilus	Mutation(s): 1 EC: 1.11.1.6
UniProt
Find proteins for M4GGR7 (Mycothermus thermophilus) Explore M4GGR7 Go to UniProtKB: M4GGR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M4GGR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HDD Query on HDD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	E [auth A], N [auth B], R [auth C], U [auth D]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	K [auth A], L [auth A], M [auth A], Q [auth B], X [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain X [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain X [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], S [auth C], T [auth C], V [auth D], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.471	α = 90
b = 120.251	β = 101.97
c = 183.665	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Yuzugullu Karakus, Y.

Funding Organization	Location	Grant Number
TUBITAK	Turkey	113Z744

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2018-08-01
Changes: Data collection, Experimental preparation
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description