+Open data
-Basic information
Entry | Database: PDB / ID: 2zgc | ||||||
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Title | Crystal Structure of Active Human Granzyme M | ||||||
Components | Granzyme M | ||||||
Keywords | HYDROLASE / Serine Protease / Cytolysis / Glycoprotein / Secreted / Zymogen | ||||||
Function / homology | Function and homology information Alternative complement activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / T cell mediated cytotoxicity / killing of cells of another organism / serine-type endopeptidase activity / innate immune response / apoptotic process / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Wu, L.F. / Wang, L. / Hua, G.Q. / Liu, K. / Zhai, Y.J. / Sun, F. / Fan, Z.S. | ||||||
Citation | Journal: J.Immunol. / Year: 2009 Title: Structural basis for proteolytic specificity of the human apoptosis-inducing granzyme M Authors: Wu, L. / Wang, L. / Hua, G. / Liu, K. / Yang, X. / Zhai, Y. / Bartlam, M. / Sun, F. / Fan, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zgc.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zgc.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zgc_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 2zgc_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 2zgc_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2zgc_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zgc ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zgc | HTTPS FTP |
-Related structure data
Related structure data | 2zghC 2zgjC 2zksC 1dstS 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: 26132.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Inclusion bodies / Source: (gene. exp.) Homo sapiens (human) / Gene: GZMM, MET1 / Plasmid: pET26b-GzmM / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: P51124, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Chemical | ChemComp-SO4 / #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: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M BICINE, 0.2M Li2SO4, 0.1M MGCL2, 19% PEG3350, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 26720 / Num. obs: 26319 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.08 / Num. unique all: 1596 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DST Resolution: 1.96→32.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.523 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.148 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.285 Å2
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Refine analyze | Luzzati coordinate error obs: 0.287 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→32.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 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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