5XZN | pdb_00005xzn

CATPO mutant - V228C

PDB DOI: https://doi.org/10.2210/pdb5XZN/pdb

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

Deposited: 2017-07-13 Released: 2018-07-18
Deposition Author(s): Yuzugullu Karakus, Y., Balci, S., Goc, G., Pearson, A.R., Yorke, B.
Funding Organization(s): The Scientific and Technological Research Council of Turkey

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.175 (Depositor), 0.180 (DCC)
R-Value Work:
0.149 (Depositor), 0.160 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

CATPO mutant - V228C

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

To be published.

Macromolecule Content

Total Structure Weight: 304.12 kDa
Atom Count: 25,490
Modeled Residue Count: 2,709
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 (Humicola insolens) 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 (Subject of Investigation/LOI) Query on HDD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	E [auth A], K [auth B], Q [auth C], W [auth D]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain N [auth B] 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 U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain N [auth B] 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 U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	AA [auth D] N [auth B] O [auth B] P [auth B] S [auth C] AA [auth D], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C], Z [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	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], L [auth B], M [auth B], R [auth C], X [auth D], Y [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 L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D] Focus chain Y [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 L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.175 (Depositor), 0.180 (DCC)
R-Value Work: 0.149 (Depositor), 0.160 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.121	α = 90
b = 121.08	β = 101.96
c = 185.119	γ = 90

Software Package:

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

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
The Scientific and Technological Research Council of Turkey	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 2.0: 2021-04-14
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description