3VUA | pdb_00003vua

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated surface determinant protein H	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q931P4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] N [auth C] O [auth C] S [auth E] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth E] Focus chain T [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B]	J [auth B] K [auth C] L [auth C] M [auth C] Q [auth D] 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		Interactions Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth E] Interactions & Density Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain I [auth A]	I [auth A], P [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.212 (Depositor), 0.212 (DCC)
R-Value Work: 0.180 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

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