4GRC

Crystal structure of DyP-type peroxidase (SCO2276) from Streptomyces coelicolor

PDB DOI: https://doi.org/10.2210/pdb4GRC/pdb

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

Deposited: 2012-08-24 Released: 2013-09-04
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: 2.00 ?
R-Value Free: 0.198
R-Value Work: 0.159
R-Value Observed: 0.161

Starting Model: experimental
View more details

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: 47.44 kDa
Atom Count: 3,200
Modelled Residue Count: 357
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein	A	440	Streptomyces coelicolor A3(2)	Mutation(s): 0 Gene Names: SCO2276 EC: 1.11.1.19 (PDB Primary Data), 1.11.1 (UniProt)
UniProt
Find proteins for Q9RKQ2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9RKQ2 Go to UniProtKB: Q9RKQ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RKQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEO Query on PEO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.198
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 71.99	α = 90
b = 71.99	β = 90
c = 170.81	γ = 120

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

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: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4GRC

Crystal structure of DyP-type peroxidase (SCO2276) from Streptomyces coelicolor

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)