4GT2

Crystal structure of DyP-type peroxidase (SCO3963) from Streptomyces coelicolor

PDB DOI: https://doi.org/10.2210/pdb4GT2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-28 Released: 2013-09-11
Deposition Author(s): Lukk, T., Hetta, A.M.A., Jones, A., Solbiati, J., Majumdar, S., Cronan, J.E., Gerlt, J.A., Nair, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185
R-Value Work: 0.147
R-Value Observed: 0.149

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DyP-type peroxidases from Stretptomyces and Thermobifida can modify organosolv lignin.

Lukk, T., Hetta, A.M.A., Jones, A., Solbiati, J., Majumdar, S., Cronan, J.E., Gerlt, J.A., Nair, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 200.41 kDa
Atom Count: 13,783
Modelled Residue Count: 1,479
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein SCO3963	A [auth B], B [auth A], C [auth E], D [auth G]	465	Streptomyces coelicolor A3(2)	Mutation(s): 0 Gene Names: SCO3963 EC: 1.11.1.19 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for Q9ZBW9 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9ZBW9 Go to UniProtKB: Q9ZBW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZBW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain J [auth A] SDF format, chain N [auth E] SDF format, chain S [auth G] MOL2 format, chain E [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth E] MOL2 format, chain S [auth G] mmCIF format, chain E [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth E] mmCIF format, chain S [auth G]	E [auth B], J [auth A], N [auth E], S [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth B] Focus chain J [auth A] Focus chain N [auth E] Focus chain S [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth B] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain R [auth E] SDF format, chain U [auth G] MOL2 format, chain F [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain R [auth E] MOL2 format, chain U [auth G] mmCIF format, chain F [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain R [auth E] mmCIF format, chain U [auth G]	F [auth B] I [auth B] K [auth A] M [auth A] O [auth E] F [auth B], I [auth B], K [auth A], M [auth A], O [auth E], P [auth E], R [auth E], U [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth E] Focus chain U [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth A] SDF format, chain Q [auth E] SDF format, chain T [auth G] MOL2 format, chain G [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth G] mmCIF format, chain G [auth B] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth G]	G [auth B], L [auth A], Q [auth E], T [auth G]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth A] Focus chain Q [auth E] Focus chain T [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.87	α = 90
b = 203.2	β = 110.73
c = 76.32	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description