+Open data
-Basic information
Entry | Database: PDB / ID: 2i7r | ||||||
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Title | conserved domain protein | ||||||
Components | Conserved domain protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / structural genomics conserved domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / Conserved domain protein / Conserved domain protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Duke, N.E.C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: conserved domain protein Authors: Duke, N.E.C. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i7r.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i7r.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 2i7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i7r_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 2i7r_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | 2i7r_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2i7r_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/2i7r ftp://data.pdbj.org/pub/pdb/validation_reports/i7/2i7r | 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: 13313.640 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q97RR3, UniProt: A0A0H2UP77*PLUS #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.85 Å3/Da / Density % sol: 56.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.100 M sodium citrate 2.00 M sodium chloride, pH 4.50, 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-BM / Wavelength: 0.979321 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Feb 27, 2005 / Details: double crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979321 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 12.7 % / Av σ(I) over netI: 8.5 / Number: 376937 / Rmerge(I) obs: 0.096 / Χ2: 1.09 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 29639 / % possible obs: 99.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 15324 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.096 / Χ2: 1.093 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.459 / Num. unique all: 2952 / Χ2: 0.828 / % possible all: 99.2 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.5 Å / D res low: 50 Å / FOM : 0.417 / FOM acentric: 0.446 / FOM centric: 0 / Reflection: 10503 / Reflection acentric: 9815 / Reflection centric: 688 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set | R cullis acentric: 2.05 / R cullis centric: 1 / Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Loc acentric: 0.3 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 9815 / Reflection centric: 688 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set shell | ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0
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Phasing MAD set site |
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Phasing MAD shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→33.56 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.846 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.208 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: 26.599 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.258 Å / Total num. of bins used: 20
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