+Open data
-Basic information
Entry | Database: PDB / ID: 3ix0 | ||||||
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Title | Crystal structure of human seminal plasma protein PSP94 | ||||||
Components | Beta-microseminoprotein | ||||||
Keywords | ANTITUMOR PROTEIN / APOPTOSIS / beta sheet / Greek key motif / Disulfide bond / Secreted / PROTEIN BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å | ||||||
Authors | Kumar, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ix0.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ix0.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ix0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ix0 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ix0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Either (Chain A and B) OR (chain C and D) make biological unit |
-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.41 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2009 / Details: MIRRORS |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage 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 parameters | Biso mean: 34.234 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.433 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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