4B7A | pdb_00004b7a

Probing the active center of catalase-phenol oxidase from Scytalidium thermophilum

PDB DOI: https://doi.org/10.2210/pdb4B7A/pdb

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

Deposited: 2012-08-17 Released: 2013-09-04
Deposition Author(s): Yuzugullu, Y., Trinh, C.H., Pearson, A.R., Ogel, Z.B., McPherson, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.150 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Probing the Active Center of Catalase-Phenol Oxidase from Scytalidium Thermophilum

Yuzugullu, Y., Trinh, C.H., Pearson, A.R., Ogel, Z.B., McPherson, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 320.53 kDa
Atom Count: 23,581
Modelled Residue Count: 2,688
Deposited Residue Count: 2,876
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-PHENOL OXIDASE	A, B, C, D	719	Mycothermus thermophilus	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for M4GGR5 (Humicola insolens) Explore M4GGR5 Go to UniProtKB: M4GGR5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M4GGR5
Sequence Annotations Expand
Reference Sequence LOADING

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 J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	E [auth A], J [auth B], N [auth C], R [auth D]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C₃₄ H₃₂ Fe N₄ O₅ UMGOPAWIGKFTRK-QQDQPIDJSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
3TR Query on 3TR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] O [auth C] F [auth A], G [auth A], K [auth B], L [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	3-AMINO-1,2,4-TRIAZOLE C₂ H₄ N₄ KLSJWNVTNUYHDU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	H [auth A], I [auth A], M [auth B], Q [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.151 (Depositor), 0.150 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.865	α = 90
b = 121.677	β = 115.5
c = 125.528	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other