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Yorodumi- PDB-2zg6: Crystal structure of Hypothetical protein; probable 2-haloalkanoi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zg6 | ||||||
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Title | Crystal structure of Hypothetical protein; probable 2-haloalkanoic acid dehalogenase from Sulfolobus tokodaii | ||||||
Components | Putative uncharacterized protein ST2620 | ||||||
Keywords | HYDROLASE / ST2620 / probable 2-haloalkanoic acid dehalogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Padmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Hypothetical protein; probable 2-haloalkanoic acid dehalogenase from Sulfolobus tokodaii Authors: Padmanabhan, B. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zg6.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zg6.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 2zg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zg6_validation.pdf.gz | 374.2 KB | Display | wwPDB validaton report |
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Full document | 2zg6_full_validation.pdf.gz | 383 KB | Display | |
Data in XML | 2zg6_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 2zg6_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zg6 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zg6 | 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: 25680.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q96X90 #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: 4.34 Å3/Da / Density % sol: 71.63 % |
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Crystal grow | Temperature: 293 K / Method: oil batch / pH: 4.2 Details: 2M Ammonium sulfate, 0.1M Phosphate Citrate, pH4.2 (Wizard II), Oil Batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97897, 0.97946, 0.9000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.35→50 Å / Num. all: 35912 / Num. obs: 35829 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.092 | ||||||||||||
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.38 / Num. unique all: 3517 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.729 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 59.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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