3AGT | pdb_00003agt

Hemerythrin-like domain of DcrH (met)

PDB DOI: https://doi.org/10.2210/pdb3AGT/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Nitratidesulfovibrio vulgaris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-06 Released: 2011-04-06
Deposition Author(s): Onoda, A., Okamoto, Y., Sugimoto, H., Mizohata, E., Inoue, T., Shiro, Y., Hayashi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.229 (Depositor), 0.211 (DCC)
R-Value Work:
0.203 (Depositor), 0.211 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3AGT

This is version 1.3 of the entry. See complete history.

Literature

Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH

Onoda, A., Okamoto, Y., Sugimoto, H., Mizohata, E., Inoue, T., Shiro, Y., Hayashi, T.

To be published.

Macromolecule Content

Total Structure Weight: 32.64 kDa
Atom Count: 2,654
Modeled Residue Count: 266
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemerythrin-like domain protein DcrH	A, B	136	Nitratidesulfovibrio vulgaris	Mutation(s): 0 Gene Names: dcrH
UniProt
Find proteins for Q726F3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q726F3 Go to UniProtKB: Q726F3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q726F3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFO Query on CFO 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]	CHLORO DIIRON-OXO MOIETY Cl Fe₂ O KBTPJIQAZMMQJH-UHFFFAOYSA-M		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: 1.40 Å
R-Value Free: 0.229 (Depositor), 0.211 (DCC)
R-Value Work: 0.203 (Depositor), 0.211 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.311	α = 95.27
b = 44.873	β = 104.2
c = 48.127	γ = 90.03

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SPACE	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.