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), 0.210 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFO	C [auth A], D [auth B]	CHLORO DIIRON-OXO MOIETY Cl Fe2 O KBTPJIQAZMMQJH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.229 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (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

Entry History 

Deposition Data

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

Revision History  

• 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