+Open data
-Basic information
Entry | Database: PDB / ID: 3ehr | ||||||
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Title | Crystal Structure of Human Osteoclast Stimulating Factor | ||||||
Components | Osteoclast-stimulating factor 1 | ||||||
Keywords | SIGNALING PROTEIN / BETA BARREL / HELIX-TURN-HELIX / SH3 / ANKYRIN REPEAT / ANK repeat / Cytoplasm / Phosphoprotein / Polymorphism / SH3 domain | ||||||
Function / homology | Function and homology information ossification / SH3 domain binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / signal transduction / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Tong, S. / Zhou, H. / Gao, Y. / Zhu, Z. / Zhang, X. / Teng, M. / Niu, L. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of human osteoclast stimulating factor Authors: Tong, S. / Zhou, H. / Gao, Y. / Zhu, Z. / Zhang, X. / Teng, M. / Niu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ehr.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ehr.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ehr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/3ehr ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3ehr | HTTPS FTP |
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-Related structure data
Related structure data | 3ehqSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24994.631 Da / Num. of mol.: 2 / Mutation: F33I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSTF1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92882 #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: 1.69 Å3/Da / Density % sol: 27.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG20000, 0.1M MES, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2005 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→51.367 Å / Num. all: 42702 / Num. obs: 21394 / % possible obs: 89.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 11.634 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EHQ Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.844 / SU B: 3.695 / SU ML: 0.11 / SU R Cruickshank DPI: 0.231 / SU Rfree: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.02 Å2 / Biso mean: 18.185 Å2 / Biso min: 5.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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