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- PDB-3ix0: Crystal structure of human seminal plasma protein PSP94 -

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Basic information

Entry
Database: PDB / ID: 3ix0
TitleCrystal structure of human seminal plasma protein PSP94
ComponentsBeta-microseminoprotein
KeywordsANTITUMOR PROTEIN / APOPTOSIS / beta sheet / Greek key motif / Disulfide bond / Secreted / PROTEIN BINDING
Function / homology
Function and homology information


extracellular space / nucleus
Similarity search - Function
N-terminal domain of TfIIb - #590 / Beta-microseminoprotein / Beta-microseminoprotein (PSP-94) / Complement Module, domain 1 / Complement Module; domain 1 / N-terminal domain of TfIIb / Single Sheet / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-microseminoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsKumar, M. / Kumar, A. / Jagtap, D.D. / Mahale, S.D.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of prostate secretory protein PSP94 shows an edge-to-edge association of two monomers to form a homodimer
Authors: Kumar, A. / Jagtap, D.D. / Mahale, S.D. / Kumar, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray diffraction analysis of human seminal plasma protein PSP94
Authors: Kumar, M. / Jagtap, D.D. / Mahale, S.D. / Prashar, V. / Kumar, A. / Das, A. / Bihani, S.C. / Ferrer, J.L. / Hosur, M.V. / Ramanadham, M.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-microseminoprotein
B: Beta-microseminoprotein
C: Beta-microseminoprotein
D: Beta-microseminoprotein


Theoretical massNumber of molelcules
Total (without water)43,1374
Polymers43,1374
Non-polymers00
Water4,342241
1
A: Beta-microseminoprotein
B: Beta-microseminoprotein


Theoretical massNumber of molelcules
Total (without water)21,5692
Polymers21,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area11840 Å2
MethodPISA
2
C: Beta-microseminoprotein
D: Beta-microseminoprotein


Theoretical massNumber of molelcules
Total (without water)21,5692
Polymers21,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-6 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.880, 107.880, 92.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsEither (Chain A and B) OR (chain C and D) make biological unit

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Components

#1: Protein
Beta-microseminoprotein / Prostate secreted seminal plasma protein / Prostate secretory protein PSP94 / PSP-94 / Seminal ...Prostate secreted seminal plasma protein / Prostate secretory protein PSP94 / PSP-94 / Seminal plasma beta-inhibin / Immunoglobulin-binding factor / IGBF / PN44


Mass: 10784.274 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Human Seminal Plasma / References: UniProt: P08118
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate pH 4.5, 0.2M lithium sulfate, 44-47% (v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2009 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.44 Å / Num. obs: 24778 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 29.12 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.041 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3528 / Rsym value: 0.184 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→39.433 Å / FOM work R set: 0.824 / SU ML: 1.84 / σ(F): 0.01 / Phase error: 24.13 / Stereochemistry target values: ML / Details: TLS refinement
RfactorNum. reflection% reflection
Rfree0.2625 1463 6.11 %
Rwork0.2106 --
obs0.2138 23955 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.627 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 34.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.977 Å20 Å2-0 Å2
2--1.977 Å2-0 Å2
3----4.923 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 0 241 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083016
X-RAY DIFFRACTIONf_angle_d1.0894047
X-RAY DIFFRACTIONf_dihedral_angle_d15.3911127
X-RAY DIFFRACTIONf_chiral_restr0.068444
X-RAY DIFFRACTIONf_plane_restr0.005517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.29891330.22412122X-RAY DIFFRACTION94
2.3822-2.47760.25571340.20712129X-RAY DIFFRACTION93
2.4776-2.59030.29721450.19972168X-RAY DIFFRACTION95
2.5903-2.72690.26591450.21232201X-RAY DIFFRACTION96
2.7269-2.89770.28561440.19712220X-RAY DIFFRACTION97
2.8977-3.12130.25281430.20642235X-RAY DIFFRACTION98
3.1213-3.43530.25151500.18012289X-RAY DIFFRACTION98
3.4353-3.93190.22621530.17582304X-RAY DIFFRACTION99
3.9319-4.95230.20831540.16952367X-RAY DIFFRACTION100
4.9523-39.43870.28881620.25682457X-RAY DIFFRACTION98
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)
10.7998-0.5215-0.30620.74720.15940.0444-0.1592-0.01270.1122-0.00650.1508-0.06710.10660.03590.00870.05860.04260.01970.004-0.00570.0366-25.660612.13017.7599
20.25570.57130.2029-0.01830.30710.3817-0.0696-0.0082-0.1136-0.00190.1235-0.03550.00470.0261-0.07210.10160.0193-0.04680.0199-0.01920.0818-23.0618-7.88889.3565
30.6238-0.3086-0.11370.57030.3397-0.1038-0.17150.0480.065-0.10820.21810.05330.10080.0217-0.03440.18330.00280.07120.03080.00310.0834-23.96269.6223-38.7581
40.53360.1362-0.17430.3640.18780.2734-0.0987-0.0883-0.0503-0.01450.14170.1278-0.04240.1616-0.03420.00870.0007-0.0205-0.0078-0.01630.0093-24.9161-10.593-35.1516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 94
2X-RAY DIFFRACTION2chain BB1 - 94
3X-RAY DIFFRACTION3chain CC1 - 94
4X-RAY DIFFRACTION4chain DD1 - 94

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