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Yorodumi- PDB-4gvw: Three-dimensional structure of the de novo designed serine hydrol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gvw | ||||||
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Title | Three-dimensional structure of the de novo designed serine hydrolase 2bfq_3, Northeast Structural Genomics Consortium (NESG) Target OR248 | ||||||
Components | De novo designed serine hydrolase | ||||||
Keywords | DE NOVO PROTEIN / HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) | ||||||
Function / homology | Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / ACETIC ACID / PHOSPHATE ION Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / BALBES / Resolution: 2.113 Å | ||||||
Authors | Kuzin, A. / Lew, S. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target OR248 Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gvw.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gvw.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/4gvw ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gvw | HTTPS FTP |
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-Related structure data
Related structure data | 2bfrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 21729.865 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MES / |
#4: Chemical | ChemComp-ACY / |
#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: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Method: microbatch under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:0.1M Ammonium Sulfate, 0.1M MES, 40% PEG 8000, microbatch under oil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2012 / Details: mirrors |
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: 2.1→50 Å / Num. obs: 10802 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 37 |
-Processing
Software |
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Refinement | Method to determine structure: BALBES Starting model: 2BFR Resolution: 2.113→41.427 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.836 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.19 Å2 / Biso mean: 32.397 Å2 / Biso min: 10.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.113→41.427 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: -12.6994 Å / Origin y: -15.0508 Å / Origin z: -16.0012 Å
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Refinement TLS group |
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