6TB2

Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH

• PDB DOI: https://doi.org/10.2210/pdb6TB2/pdb

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Cricetulus griseus, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-31 Released: 2019-12-18 
• Deposition Author(s): Mikkelsen, J.H., Andersen, C.B.F.
• Funding Organization(s): Lundbeckfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 

Starting Models: experimental

Literature

Haptoglobin is an inhibitor of Staphylococcus aureus IsdH-mediated heme-sequestering

Mikkelsen, J.H., Runager, K.S., Andersen, C.B.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 144 kDa 
• Atom Count: 9,750 
• Modelled Residue Count: 1,209 
• Deposited Residue Count: 1,262 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
GTEx:  ENSG00000244734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Haptoglobin	C	267	Homo sapiens	Mutation(s): 0  Gene Names: HP
UniProt & NIH Common Fund Data Resources
Find proteins for P00738 (Homo sapiens) Explore P00738  Go to UniProtKB:  P00738
GTEx:  ENSG00000257017

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell wall surface anchor family protein	D, E	354	Staphylococcus aureus	Mutation(s): 0  Gene Names: isdH, EP54_00915, EQ90_06455, HMPREF3211_02292, NCTC10654_01789
UniProt
Find proteins for Q2FXJ2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXJ2  Go to UniProtKB:  Q2FXJ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	F [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.1	α = 90
b = 86.77	β = 90
c = 217.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Mikkelsen, J.H., Andersen, C.B.F.

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Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	R191-2015-733

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description