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Yorodumi- PDB-3on2: Structure of a protein with unknown function from Rhodococcus sp. RHA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3on2 | ||||||
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Title | Structure of a protein with unknown function from Rhodococcus sp. RHA1 | ||||||
Components | Probable transcriptional regulator | ||||||
Keywords | structural genomics / unknown function / Protein Structure Initiative / PSI-2 / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus jostii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å | ||||||
Authors | Fan, Y. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a protein with unknown function from Rhodococcus sp. RHA1 Authors: Fan, Y. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3on2.cif.gz | 339.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3on2.ent.gz | 293 KB | Display | PDB format |
PDBx/mmJSON format | 3on2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3on2_validation.pdf.gz | 994.7 KB | Display | wwPDB validaton report |
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Full document | 3on2_full_validation.pdf.gz | 1006.1 KB | Display | |
Data in XML | 3on2_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 3on2_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3on2 ftp://data.pdbj.org/pub/pdb/validation_reports/on/3on2 | 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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-Components
#1: Protein | Mass: 21043.119 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro01040 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SHW9 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PG6 / #4: 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: 2.24 Å3/Da / Density % sol: 45.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2M Li sulfate, 0.1M Bis-Tris pH6.2, 29% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2010 / Details: mirror |
Radiation | Monochromator: Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 53066 / Num. obs: 53066 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 6.18 / Num. unique all: 2557 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.011 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.704 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.956→2.007 Å / Total num. of bins used: 20
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