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- PDB-3r8j: Crystal structure of human SOUL protein (orthorhombic form) -

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Basic information

Entry
Database: PDB / ID: 3r8j
TitleCrystal structure of human SOUL protein (orthorhombic form)
ComponentsHeme-binding protein 2
KeywordsAPOPTOSIS / HEBP family / SOUL protein
Function / homology
Function and homology information


azurophil granule lumen / heme binding / Neutrophil degranulation / mitochondrion / extracellular exosome / extracellular region / 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
PHOSPHATE ION / Heme-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsAmbrosi, E.K. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL.
Authors: Ambrosi, E. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein 2
B: Heme-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4213
Polymers47,3262
Non-polymers951
Water7,098394
1
A: Heme-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7582
Polymers23,6631
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)23,6631
Polymers23,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.720, 114.660, 67.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Heme-binding protein 2 / Placental protein 23 / PP23 / Protein SOUL


Mass: 23663.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf34, HEBP2, SOUL / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C41 / References: UniProt: Q9Y5Z4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: KH2PO4 0.8M, NaH2PO4 0.8M, HEPES 0.08M, 1-butyl-3-methylimidazolium chloride 0.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2009
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→24.9 Å / Num. all: 70506 / Num. obs: 69655 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.6 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→24.866 Å / SU ML: 0.18 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3519 5.05 %Random
Rwork0.1749 ---
all0.1761 69663 --
obs0.1761 69648 98.78 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.465 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7243 Å20 Å2-0 Å2
2--3.3728 Å20 Å2
3----4.0972 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 5 394 3261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083077
X-RAY DIFFRACTIONf_angle_d1.254219
X-RAY DIFFRACTIONf_dihedral_angle_d11.9931193
X-RAY DIFFRACTIONf_chiral_restr0.081455
X-RAY DIFFRACTIONf_plane_restr0.006554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.26723420.24766441X-RAY DIFFRACTION98
1.6572-1.72350.23633560.2136536X-RAY DIFFRACTION98
1.7235-1.80190.21743530.1846491X-RAY DIFFRACTION99
1.8019-1.89690.19263610.16896530X-RAY DIFFRACTION99
1.8969-2.01570.19453340.16776590X-RAY DIFFRACTION99
2.0157-2.17130.17273330.16686601X-RAY DIFFRACTION99
2.1713-2.38960.18733370.16396678X-RAY DIFFRACTION99
2.3896-2.7350.20093730.17846661X-RAY DIFFRACTION99
2.735-3.44440.19423590.17636732X-RAY DIFFRACTION100
3.4444-24.8690.19093710.16696869X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -18.4342 Å / Origin y: -17.788 Å / Origin z: -24.5993 Å
111213212223313233
T0.0671 Å2-0.0336 Å2-0.0059 Å2-0.0782 Å20.0121 Å2--0.0828 Å2
L-0.0116 °2-0.0643 °20.0498 °2-0.0921 °20.1195 °2--0.9468 °2
S0.0072 Å °0.0001 Å °-0.002 Å °0.0057 Å °0.0187 Å °0.0136 Å °0.041 Å °-0.0055 Å °-0.0232 Å °
Refinement TLS groupSelection details: all

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