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Yorodumi- PDB-1o5j: Crystal structure of Periplasmic divalent cation tolerance protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o5j | ||||||
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Title | Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution | ||||||
Components | periplasmic divalent cation tolerance protein | ||||||
Keywords | UNKNOWN FUNCTION / TM1056 / PERIPLASMIC DIVALENT CATION TOLERANCE PROTEIN / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o5j.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o5j.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/1o5j ftp://data.pdbj.org/pub/pdb/validation_reports/o5/1o5j | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13748.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0E6 |
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#2: 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: 2.05 Å3/Da / Density % sol: 39.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 10.5 Details: 30% PEG-400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97944, 0.97924, 0.95658 | ||||||||||||
Detector | Type: APS / Detector: CCD / Date: Oct 25, 2002 Details: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | ||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→45.48 Å / Num. obs: 7337 / % possible obs: 100 % / Redundancy: 7.49 % / Biso Wilson estimate: 41.58 Å2 / Rsym value: 0.068 / Net I/σ(I): 32.91 | ||||||||||||
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.99 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 563 / Rsym value: 0.245 / % possible all: 70.02 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→45.48 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.47 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→45.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.002 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.464 Å / Origin y: 52.935 Å / Origin z: 24.378 Å
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Refinement TLS group | Selection: ALL |