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Yorodumi- PDB-2zgj: Crystal Structure of D86N-GzmM Complexed with Its Optimal Synthes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zgj | ||||||
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Title | Crystal Structure of D86N-GzmM Complexed with Its Optimal Synthesized Substrate | ||||||
Components |
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Keywords | HYDROLASE / Serine protease / synthesized peptide / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 2zgj.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zgj.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zgj_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 2zgj_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 2zgj_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2zgj_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zgj ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zgj | HTTPS FTP |
-Related structure data
Related structure data | 2zgcSC 2zghC 2zksC 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: 26131.562 Da / Num. of mol.: 1 / Mutation: D86N Source method: isolated from a genetically manipulated source Details: Refolding from inclusion bodies / Source: (gene. exp.) Homo sapiens (human) / Gene: GZMM, MET1 / Plasmid: pET26b-D86N-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: Protein/peptide | Mass: 774.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 3.35 Å3/Da / Density % sol: 63.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Bicine, 0.2M Li2SO4, 21% PEG3350, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 16708 / Num. obs: 16608 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.38 / Num. unique all: 1080 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZGC Resolution: 2.3→26.45 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.407 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.236 / 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: 49.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→26.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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