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Yorodumi- PDB-4ne7: Crystal Structure of engineered Kumamolisin-As from Alicyclobacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ne7 | ||||||
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Title | Crystal Structure of engineered Kumamolisin-As from Alicyclobacillus sendaiensis, Northeast Structural Genomics Consortium (NESG) Target OR367 | ||||||
Components | Kumamolisin-As | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ENGINEERED PROTEIN | ||||||
Function / homology | Function and homology information tripeptidyl-peptidase activity / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Alicyclobacillus sendaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å | ||||||
Authors | Guan, R. / Pultz, I.S. / Siegel, J.B. / Seetharaman, J. / Kornhaber, G. / Maglaqui, M. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. ...Guan, R. / Pultz, I.S. / Siegel, J.B. / Seetharaman, J. / Kornhaber, G. / Maglaqui, M. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target OR367 Authors: Guan, R. / Pultz, I.S. / Seetharaman, J. / Kornhaber, G. / Mao, L. / Xiao, R. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ne7.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ne7.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ne7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ne7_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 4ne7_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 4ne7_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4ne7_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/4ne7 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/4ne7 | HTTPS FTP |
-Related structure data
Related structure data | 1sn7S 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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Components on special symmetry positions |
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Details | monomer,37.57 kD,90.1% |
-Components
#1: Protein | Mass: 39068.934 Da / Num. of mol.: 1 / Fragment: UNP residues 190-553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria) Gene: scpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GB88*PLUS | ||
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#2: Chemical | ChemComp-ZN / #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: 3.45 Å3/Da / Density % sol: 64.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 15% PEG 8000, 0.1 M MES pH 6.0, 0.2 M Zinc Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.8 Å / Num. all: 19077 / Num. obs: 19077 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 34.05 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 24.83 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 9.29 / Num. unique all: 1882 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SN7 Resolution: 2.497→44.789 Å / Occupancy max: 1 / Occupancy min: 0.56 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.72 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.48 Å2 / Biso mean: 35.053 Å2 / Biso min: 4.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.497→44.789 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: 13
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