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Yorodumi- PDB-3esh: Crystal structure of a probable metal-dependent hydrolase from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3esh | ||||||
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Title | Crystal structure of a probable metal-dependent hydrolase from Staphylococcus aureus. Northeast Structural Genomics target ZR314 | ||||||
Components | Protein similar to metal-dependent hydrolase | ||||||
Keywords | HYDROLASE / Similar to metal-dependent hydrolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable metal-dependent hydrolase from Staphylococcus aureus. Northeast Structural Genomics target ZR314 Authors: Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, 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 | 3esh.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esh.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 3esh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esh_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 3esh_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 3esh_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 3esh_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esh ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32635.135 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Gene: SAV1747 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99TB7, UniProt: A0A0H3JZW1*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.17% 2,6-Naphthalenedisulfonic acid 0.17% 2,7-Naphthalenedisulfonic acid 0.17% Anthraquinone-2,6-disulfonic acid 25 mM HEPES sodium pH 6.8 6.25% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2008 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 449114 / Num. obs: 85257 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.076 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.39→2.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 11.2 / Rsym value: 0.23 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→45.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 150252.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7971 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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