+Open data
-Basic information
Entry | Database: PDB / ID: 2g4v | ||||||
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Title | anomalous substructure of proteinase K | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / anomalous substructure of proteinase K | ||||||
Function / homology | Function and homology information peptidase K / cellular anatomical entity / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Engyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATES THAT AMINO ACID 207 WAS MUTATED BY PERSUING ELECTRON DENSITY AT ATOMIC ...SEQUENCE AUTHOR STATES THAT AMINO ACID 207 WAS MUTATED BY PERSUING ELECTRON DENSITY AT ATOMIC RESOLUTION AND AFTER REPEATION OF MANY REFINEMENT CYCLE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4v.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4v.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 2g4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4v ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4v | HTTPS FTP |
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-Related structure data
Related structure data | 2g4hC 2g4iC 2g4jC 2g4kC 2g4lC 2g4mC 2g4nC 2g4oC 2g4pC 2g4qC 2g4rC 2g4sC 2g4tC 2g4uC 2g4wC 2g4xC 2g4yC 2g4zC 2g51C 2g52C 2g55C 2illC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.02 Å3/Da / Density % sol: 39.1 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→30 Å / Num. obs: 13684 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.14→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.999 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.176 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.808 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.195 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.1659 Å / Origin y: 12.972 Å / Origin z: 25.2282 Å
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