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- PDB-3d7n: The crystal structure of the flavodoxin, WrbA-like protein from A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d7n | ||||||
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Title | The crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens | ||||||
![]() | Flavodoxin, WrbA-like protein | ||||||
![]() | ELECTRON TRANSPORT / flavodoxin / WrbA-like protein / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of the flavodoxin, WrbA-like protein from Agrobacterium tumefaciens Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / 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 | ![]() | 39.4 KB | Display | ![]() |
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PDB format | ![]() | 30.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 398.7 KB | Display | ![]() |
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Full document | ![]() | 402.9 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 7.8 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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1 | ![]()
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Unit cell |
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Details | This protein exists as tetramer. The rest part of the biological assembly is generated by the operations:x-y,-y,-z+1; -x+1,-y,z; -x+y+1,y,-z+1 |
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Components
#1: Protein | Mass: 20944.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes, 0.2M NaCl, 25%PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 22, 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: 2.3→58.52 Å / Num. all: 10480 / Num. obs: 10224 / % possible obs: 97.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.7 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 17.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.45 / Num. unique all: 781 / % possible all: 92.32 |
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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: 47.774 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→58.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 25.2885 Å / Origin y: 12.5357 Å / Origin z: 77.9606 Å
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Refinement TLS group |
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