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Yorodumi- PDB-1tza: X-ray structure of Northeast Structural Genomics Consortium targe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tza | ||||||
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Title | X-ray structure of Northeast Structural Genomics Consortium target SoR45 | ||||||
Components | apaG protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Kuzin, A.P. / Vorobiev, S.M. / Edstrom, W. / Acton, T.B. / Shastry, R. / Ma, L.-C. / Cooper, B. / Xiao, R. / Montelione, G. / Tong, L. ...Kuzin, A.P. / Vorobiev, S.M. / Edstrom, W. / Acton, T.B. / Shastry, R. / Ma, L.-C. / Cooper, B. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray structure of Northeast Structural Genomics Consortium target SoR45 Authors: Kuzin, A.P. / Vorobiev, S.M. / Edstrom, W. / Acton, T.B. / Shastry, R. / Ma, L.-C. / Cooper, B. / Xiao, R. / Montelione, G. / 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 | 1tza.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tza.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tza_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 1tza_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 1tza_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1tza_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tza ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tza | 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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Unit cell |
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-Components
#1: Protein | Mass: 15036.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EB92 #2: Chemical | ChemComp-CAC / | #3: 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: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: 8% PEG4000, 0.05mM Cacodylic Acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97868 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97868 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 10774 / Num. obs: 10666 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 8.93 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 52.23 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 37.83 / Num. unique all: 1140 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→29.67 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 597383.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9162 Å2 / ksol: 0.410325 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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