6I91 | pdb_00006i91

Dye type peroxidase Aa from Streptomyces lividans: 156.8 kGy structure

PDB DOI: https://doi.org/10.2210/pdb6I91/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lividans 1326
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-22 Released: 2019-12-04
Deposition Author(s): Ebrahim, A., Moreno-Chicano, T., Worrall, J.A.R., Strange, R.W., Axford, D., Sherrell, D.A., Appleby, M., Owen, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6I91

Ligand Structure Quality Assessment

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

Literature

Dose-resolved serial synchrotron and XFEL structures of radiation sensitive metalloproteins

Ebrahim, A., Moreno-Chicano, T., Appleby, M.V., Chaplin, A.K., Beale, J., Sherrell, D.A., Duyvesteyn, H.M.E., Owada, S., Tono, K., Sugimoto, S., Strange, R.W., Worrall, J.A.R., Axford, D., Owen, R., Hough, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 79.78 kDa
Atom Count: 6,133
Modeled Residue Count: 723
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase/peroxidase	A, B	362	Streptomyces lividans 1326	Mutation(s): 0 Gene Names: SCO2276 EC: 1.11.1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RKQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.042	α = 90
b = 68.368	β = 105.76
c = 74.974	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
cctbx.prime	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-12-04

Deposition Author(s):

Moreno-Chicano, T.

Worrall, J.A.R.

Revision History (Full details and data files)

Version 1.0: 2019-12-04
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.