+Open data
-Basic information
Entry | Database: PDB / ID: 2r0k | ||||||
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Title | Protease domain of HGFA with inhibitor Fab58 | ||||||
Components |
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Keywords | HYDROLASE / IMMUNE SYSTEM / serine protease / antibody / inhibitor / EGF-like domain / Glycoprotein / Kringle / Secreted / Zymogen | ||||||
Function / homology | Function and homology information MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Eigenbrot, C. / Shia, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural insight into distinct mechanisms of protease inhibition by antibodies. Authors: Wu, Y. / Eigenbrot, C. / Liang, W.C. / Stawicki, S. / Shia, S. / Fan, B. / Ganesan, R. / Lipari, M.T. / Kirchhofer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r0k.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r0k.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 2r0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r0k_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 2r0k_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 2r0k_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 2r0k_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/2r0k ftp://data.pdbj.org/pub/pdb/validation_reports/r0/2r0k | HTTPS FTP |
-Related structure data
Related structure data | 2r0lC 1fvdS 1ybwS 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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Unit cell |
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-Components
#1: Protein | Mass: 30885.154 Da / Num. of mol.: 1 / Fragment: HGFA protease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Antibody | Mass: 23287.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 23688.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis. Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.12 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 9.5 Details: 1:1 mixture of protein complex solution and reservoir containing 1.0M K/Na tartrate, CHES pH9.5, 0.2M Lithium Sulfate, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2007 |
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: 3.5→50 Å / Num. all: 10827 / Num. obs: 10827 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.8 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb 1YBW, pdb 1FVD Resolution: 3.51→50 Å / Cor.coef. Fo:Fc: 0.83 / Cor.coef. Fo:Fc free: 0.746 / SU B: 81.71 / SU ML: 0.585 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -2 / ESU R Free: 0.813 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 16.411 Å2
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Refinement step | Cycle: LAST / Resolution: 3.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.508→3.599 Å / Total num. of bins used: 20
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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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