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Yorodumi- PDB-4nar: Crystal Structure of the Q9WYS3 protein from Thermotoga maritima.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nar | ||||||
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Title | Crystal Structure of the Q9WYS3 protein from Thermotoga maritima. Northeast Structural Genomics Consortium Target VR152 | ||||||
Components | Putative uronate isomerase | ||||||
Keywords | ISOMERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / VR152 / PF09861 / DUF2088 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.388 Å | ||||||
Authors | Vorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / 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: Crystal Structure of the Q9WYS3 protein from Thermotoga maritima. Authors: Vorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / 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 | 4nar.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nar.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nar_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 4nar_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 4nar_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 4nar_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/4nar ftp://data.pdbj.org/pub/pdb/validation_reports/na/4nar | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 50666.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589/MSB8/DSM 3109/JCM 10099 / Gene: Tmari_0439, TM_0442 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9WYS3 | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: 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: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 291 K / Method: microbatch crystallization under oil / pH: 4.6 Details: 30% PEG MME 2000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, Microbatch crystallization under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. all: 18378 / Num. obs: 18360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1807 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.388→47.023 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.168 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.92 Å2 / Biso mean: 31.386 Å2 / Biso min: 10.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.388→47.023 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: 12
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Refinement TLS params. | Method: refined / Origin x: -17.1145 Å / Origin y: 23.9907 Å / Origin z: -13.4147 Å
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Refinement TLS group | Selection details: chain A |