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Yorodumi- PDB-2r6u: Crystal structure of gene product RHA04853 from Rhodococcus sp. RHA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r6u | ||||||
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Title | Crystal structure of gene product RHA04853 from Rhodococcus sp. RHA1 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / RHA04853 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of gene product RHA04853 from Rhodococcus sp. RHA1. Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.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 | 2r6u.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r6u.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r6u ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r6u | 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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2 |
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Unit cell |
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Details | This protein existed as dimer. There are two dimers in the asymmtric unit: Mol.A/Mol.C, Mol.B/Mol.D |
-Components
#1: Protein | Mass: 16116.764 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA04853, RHA1_ro04536 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0S814 #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: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Na(OAC), 0.2M Ammonium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→58.72 Å / Num. all: 80327 / Num. obs: 79299 / % possible obs: 98.72 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.5→1.538 Å / Redundancy: 7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.85 / Num. unique all: 5882 / % possible all: 88.54 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→58.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.327 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.077 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 16.334 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→58.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -10.877 Å / Origin y: 34.26 Å / Origin z: 45.823 Å
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Refinement TLS group |
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