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- PDB-2gov: Solution structure of Murine p22HBP -

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Basic information

Entry
Database: PDB / ID: 2gov
TitleSolution structure of Murine p22HBP
ComponentsHeme-binding protein 1
KeywordsHEME BINDING PROTEIN / p22HBP / heme binding / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
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 / cytosol / cytoplasm
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 / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Dias, J.S. / Goodfellow, B.J. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: The First Structure from the SOUL/HBP Family of Heme-binding Proteins, Murine P22HBP.
Authors: Dias, J.S. / Macedo, A.L. / Ferreira, G.C. / Peterson, F.C. / Volkman, B.F. / Goodfellow, B.J.
#1: Journal: J.Biomol.Nmr / Year: 2005
Title: 1H, 15N and 13C resonance assignments of the heme-binding protein murine p22HBP.
Authors: Dias, J.S. / Macedo, A.L. / Ferreira, G.C. / Jeanty, N. / Taketani, S. / Goodfellow, B.J. / Peterson, F.C. / Volkman, B.F.
History
DepositionApr 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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_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 / _struct_ref_seq_dif.details

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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)21,7771
Polymers21,7771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Heme-binding protein 1 / p22HBP


Mass: 21777.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hebp1, Hbp / Plasmid: pNJ2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): 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
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE.

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Sample preparation

DetailsContents: 1.0 mM p22HBP U-15N/13C, 50 mM sodium phosphate / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 28 mM / pH: 8.0 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,F. et al.processing
XEASY1.3Eccles, C.; Guntert, P.; Billeter, M.; Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
Xplor-NIH2.9.3SCHWIETERS, C.D., KUSZEWSKI, J.J., TJANDRA, N., CLORE, G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1851 NOE CONSTRAINTS ( 372 INTRA, 425 SEQUENTIAL, 276 MEDIUM and 778 LONG RANGE CONSTRAINTS) AND 276 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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