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Yorodumi- PDB-1t82: Crystal Structure of the putative thioesterase from Shewanella on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t82 | ||||||
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Title | Crystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51 | ||||||
Components | hypothetical acetyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics / alpha-beta dimeric protein with a fold resembling a hotdog / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Thioesterase, putative / Putative thioesterase (yiiD_Cterm) / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / acyltransferase activity, transferring groups other than amino-acyl groups / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase domain protein YiiD Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51 Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t82.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t82.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t82_validation.pdf.gz | 457.5 KB | Display | wwPDB validaton report |
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Full document | 1t82_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 1t82_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1t82_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t82 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t82 | 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: 17851.510 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Plasmid: BL21(DE3)+Magic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8E989 #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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 10mM Tris, 100mM NaCl, 5mM DTT. Reservoir solution: 20% PEG 3350, 200mM sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.81 Å / Num. all: 112723 / Num. obs: 107847 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.43 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.079 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 9.73 / Num. unique all: 15130 / Rsym value: 0.171 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→29.81 Å Isotropic thermal model: anisotropic and overall temperature factors Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
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Displacement parameters | Biso mean: 15.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.005
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