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- PDB-7oon: The X-ray structure of heme-bound murine HEBP1 -

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Basic information

Entry
Database: PDB / ID: 7oon
TitleThe X-ray structure of heme-bound murine HEBP1
ComponentsHeme-binding protein 1
KeywordsAPOPTOSIS / Heme-binding protein
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 / Regulatory factor, effector binding domain superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Birck, C. / Goodfellow, B.J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: Coord. Chem. Rev / Year: 2021
Title: The SOUL family of heme-binding proteins: Structure and function 15 years later
Authors: Goodfellow, B.J. / Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Delgado, L. / Ferreira, G.C. / Rodrigues, J.E. / Poussin-Courmontagne, P. / Birck, C. / McEwen, A. / Macedo, A.L.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme-binding protein 1
B: Heme-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4576
Polymers41,0322
Non-polymers1,4254
Water55831
1
A: Heme-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3254
Polymers20,5161
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1322
Polymers20,5161
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.493, 79.492, 85.074
Angle α, β, γ (deg.)90.000, 102.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

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Components

#1: Protein Heme-binding protein 1 / p22HBP


Mass: 20515.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 7-190 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hebp1, Hbp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R257
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 5000 MME, 0.1 M MES pH 6.5, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.78→48.94 Å / Num. obs: 19098 / % possible obs: 93.5 % / Redundancy: 2.597 % / Biso Wilson estimate: 76.91 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.185 / Χ2: 0.768 / Net I/σ(I): 5.78 / Num. measured all: 49603
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.78-2.952.5081.8620.637559332330140.1342.34590.7
2.95-3.162.581.0971.247732308929970.3521.38197
3.16-3.412.5380.6262.326844290426970.6610.78992.9
3.41-3.732.7180.3584.316722264224730.8620.44793.6
3.73-4.172.70.187.175938239721990.9580.22591.7
4.17-4.812.6020.09111.15068209419480.9810.11593
4.81-5.872.6530.08311.984564180317200.9820.10495.4
5.87-8.252.5560.06712.973307138812940.9910.08493.2
8.25-48.942.4720.0517.3918697937560.9930.06395.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.5.25data scaling
PDB_EXTRACT3.27data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R8J

3r8j


Resolution: 2.8→48.94 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0.47 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 893 4.72 %
Rwork0.2101 18021 -
obs0.2112 18914 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.63 Å2 / Biso mean: 101.8774 Å2 / Biso min: 39.31 Å2
Refinement stepCycle: final / Resolution: 2.8→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 96 31 2963
Biso mean--87.27 71.23 -
Num. residues----369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.980.34741690.36013067323697
2.98-3.210.35561120.32263110322296
3.21-3.530.31781480.29312950309893
3.53-4.040.30561510.2092921307292
4.04-5.090.17921410.16162984312594
5.09-48.940.17451720.1732989316194
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1632-0.41930.68373.68060.14281.07460.22330.0172-0.28540.0878-0.12541.06360.07560.12420.02860.33690.019-0.03440.524-0.06760.738352.532-0.2696122.8919
20.91520.24210.21210.92740.12591.69970.36020.33370.2485-1.556-0.31950.0668-0.15120.04950.12581.63360.33990.04120.80980.03880.545365.915515.865195.3516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' )A0
2X-RAY DIFFRACTION2(chain 'B' )B0

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