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Yorodumi- PDB-3b4s: Crystal structure of a LuxT domain from Vibrio parahaemolyticus R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b4s | ||||||
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Title | Crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633 | ||||||
Components | Protein LuxT | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC91483.1 / LuxT domain / Vibrio parahaemolyticus RIMD 2210633 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus RIMD 2210633 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Tan, K. / Zhou, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a LuxT domain from Vibrio parahaemolyticus RIMD 2210633. Authors: Tan, K. / Zhou, M. / Gu, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b4s.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b4s.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b4s_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
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Full document | 3b4s_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 3b4s_validation.xml.gz | 26 KB | Display | |
Data in CIF | 3b4s_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b4s ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b4s | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | Authors state that the biological unit is experimentally unknown. It is likely a hexamer with the assembly shown in remark 350. |
-Components
#1: Protein | Mass: 10917.929 Da / Num. of mol.: 8 / Fragment: LuxT domain: Residues 63-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria) Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0420 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87J33 |
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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: 4.58 Å3/Da / Density % sol: 73.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis-tris propane, 1.3M di-Ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97948 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2007 / Details: Mirrors | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→48.22 Å / Num. all: 29395 / Num. obs: 29395 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 85.8 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 23.3 | |||||||||
Reflection shell | Resolution: 3.1→3.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2453 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.1→48.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.697 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.707 / ESU R Free: 0.337 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.169 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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