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- PDB-2hva: Solution Structure of the haem-binding protein p22HBP -

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Basic information

Entry
Database: PDB / ID: 2hva
TitleSolution Structure of the haem-binding protein p22HBP
ComponentsHeme-binding protein 1
KeywordsLIGAND BINDING PROTEIN / haem-binding protein / beta-beta-alpha-beta-beta repeat / hydrophobic-ligand binding domain
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / heme metabolic process / G alpha (i) signalling events / heme binding / mitochondrion / cytoplasm / cytosol
Similarity search - Function
SOUL haem-binding protein / SOUL heme-binding protein / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Heme-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Simulated annealing with torsion angle dynamics
Model type detailsminimized average
AuthorsGell, D.A. / Mackay, J.P. / Westman, B.J. / Liew, C.K. / Gorman, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Novel Haem-binding Interface in the 22 kDa Haem-binding Protein p22HBP.
Authors: Gell, D.A. / Westman, B.J. / Gorman, D. / Liew, C.K. / Welch, J.J. / Weiss, M.J. / Mackay, J.P.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 8, 2006ID: 2HC6
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein 1


Theoretical massNumber of molelcules
Total (without water)21,2191
Polymers21,2191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 200structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Heme-binding protein 1 / 22 kDa haem-binding protein / p22HBP / hebp1


Mass: 21218.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hebp1, Hbp / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): K12 BL21(DE3) / References: UniProt: Q9R257

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1212D NOESY
1323D 13C-separated NOESY
NMR detailsText: The structure was determined using standard triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM p22HBP U95%-15N, U95%-13C; 20mM Na2HPO4/NaH2PO4; 0.002mM 5,5-dimethylsilapentanesulfonate; pH 6.2; 95% H2O, 5% D2O95% H2O/5% D2O
21mM p22HBP U95%-15N, U95%-13C; 20mM Na2HPO4/NaH2PO4; 0.002mM 5,5-dimethylsilapentanesulfonate; pH 6.2; 98% D2O98% D2O
Sample conditionsIonic strength: 20mM sodium phosphate / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5 patchlevel 6Bruker Biospincollection
Sparky3.11T.D. Goddard and D.G. Knellerdata analysis
CNS1.1A.T. Brungerrefinement
RefinementMethod: Simulated annealing with torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 21

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