+Open data
-Basic information
Entry | Database: PDB / ID: 2asu | ||||||
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Title | Crystal Structure of the beta-chain of HGFl/MSP | ||||||
Components | (Hepatocyte growth factor-like protein) x 2 | ||||||
Keywords | HYDROLASE / serine proteinase / beta-chain / MSP / HGFl | ||||||
Function / homology | Function and homology information Signaling by MST1 / regulation of cAMP-dependent protein kinase activity / regulation of receptor signaling pathway via JAK-STAT / negative regulation of gluconeogenesis / receptor tyrosine kinase binding / collagen-containing extracellular matrix / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Carafoli, F. / Chirgadze, D.Y. / Blundell, T.L. / Gherardi, E. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: Crystal structure of the beta-chain of human hepatocyte growth factor-like/macrophage stimulating protein. Authors: Carafoli, F. / Chirgadze, D.Y. / Blundell, T.L. / Gherardi, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2asu.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2asu.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 2asu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2asu_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 2asu_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2asu_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2asu_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2asu ftp://data.pdbj.org/pub/pdb/validation_reports/as/2asu | HTTPS FTP |
-Related structure data
Related structure data | 1buiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2398.835 Da / Num. of mol.: 1 / Fragment: alpha-chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MST1, HGFL / Plasmid: pA71d / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: P26927 |
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#2: Protein | Mass: 25955.918 Da / Num. of mol.: 1 / Fragment: beta-chain / Mutation: C672S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MST1, HGFL / Plasmid: pA71d / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: P26927 |
#3: 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: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.1 Details: 1.4 M NaH2PO4, 0.93 M K2HPO4, CAPS pH 10.5, Li2SO4 0.1 M, pH 6.1, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 23920 / Num. obs: 23920 / % possible obs: 98.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.416 / Rsym value: 0.416 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BUI Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.129 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.845→1.893 Å / Total num. of bins used: 20
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