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Yorodumi- PDB-1sfp: CRYSTAL STRUCTURE OF ACIDIC SEMINAL FLUID PROTEIN (ASFP) AT 1.9 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sfp | ||||||
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Title | CRYSTAL STRUCTURE OF ACIDIC SEMINAL FLUID PROTEIN (ASFP) AT 1.9 A RESOLUTION: A BOVINE POLYPEPTIDE FROM THE SPERMADHESIN FAMILY | ||||||
Components | ASFP | ||||||
Keywords | SPERMADHESIN / BOVINE SEMINAL PLASMA PROTEIN / ACIDIC SEMINAL FLUID PROTEIN / ASFP / CUB DOMAIN / X-RAY CRYSTAL STRUCTURE / GROWTH FACTOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.9 Å | ||||||
Authors | Romao, M.J. / Kolln, I. / Dias, J.M. / Carvalho, A.L. / Romero, A. / Varela, P.F. / Sanz, L. / Topfer-Petersen, E. / Calvete, J.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: The crystal structures of two spermadhesins reveal the CUB domain fold. Authors: Romero, A. / Romao, M.J. / Varela, P.F. / Kolln, I. / Dias, J.M. / Carvalho, A.L. / Sanz, L. / Topfer-Petersen, E. / Calvete, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sfp.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sfp.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sfp_validation.pdf.gz | 366.2 KB | Display | wwPDB validaton report |
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Full document | 1sfp_full_validation.pdf.gz | 365.4 KB | Display | |
Data in XML | 1sfp_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 1sfp_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/1sfp ftp://data.pdbj.org/pub/pdb/validation_reports/sf/1sfp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12932.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASFP / Source: (natural) Bos taurus (cattle) / Secretion: SEMINAL PLASMA / References: UniProt: P29392 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: AMMONIUM SULFATE, PH 4.7, POLYETHYLENEGLYCOL 4000, 10% DIOXANE | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 8773 / % possible obs: 94.8 % / Redundancy: 5.1 % / Rsym value: 0.082 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 98 |
Reflection | *PLUS Num. measured all: 44844 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.9→10 Å / Num. parameters: 3839 / Num. restraintsaints: 3634 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 948 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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