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Open data
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Basic information
Entry | Database: PDB / ID: 2i7r | ||||||
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Title | conserved domain protein | ||||||
![]() | Conserved domain protein | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duke, N.E.C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.7 KB | Display | ![]() |
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Full document | ![]() | 434.5 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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Refinement | Method to determine structure: ![]() 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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