3VUA

Apo IsdH-NEAT3 in space group P3121 at a resolution of 1.85 A

• PDB DOI: https://doi.org/10.2210/pdb3VUA/pdb

• Classification: HEME-BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-26 Released: 2013-06-26 
• Deposition Author(s): Vu, N.T., Caaveiro, J.M.M., Moriwaki, Y., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin

Vu, N.T., Moriwaki, Y., Caaveiro, J.M.M., Tsumoto, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 7 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.87 kDa 
• Atom Count: 6,343 
• Modelled Residue Count: 683 
• Deposited Residue Count: 756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated surface determinant protein H	A, B, C, D, E, F	126	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: harA, isdH, IsdH-NEAT3, sasI, SAV1731
UniProt
Find proteins for Q931P4 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q931P4  Go to UniProtKB:  Q931P4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], N [auth C], O [auth C], S [auth E], T [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B], K [auth C], L [auth C], M [auth C], Q [auth D], R [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	I [auth A], P [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.68	α = 90
b = 126.68	β = 90
c = 116.591	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Vu, N.T., Caaveiro, J.M.M., Moriwaki, Y., Tsumoto, K.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description