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- PDB-1vki: Crystal structure of a putative oligo-nucleotide binding protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vki | ||||||
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Title | Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution | ||||||
![]() | HYPOTHETICAL PROTEIN ATU3699 | ||||||
![]() | TRANSLATION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of hypothetical protein (ATU3699) from Agrobacterium tumefaciens at 1.60 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.3 KB | Display | ![]() |
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Full document | ![]() | 441 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vjfS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 5 - 169 / Label seq-ID: 17 - 181
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Components
#1: Protein | Mass: 20051.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Gene: ATU3699 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop Details: 20.025% PEG 8000, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Oct 1, 2003 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 44165 / % possible obs: 95.39 % / Redundancy: 2.56 % / Biso Wilson estimate: 20.66 Å2 / Rsym value: 0.051 / Net I/σ(I): 19.88 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.76 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3277 / Rsym value: 0.303 / % possible all: 71.07 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VJF Resolution: 1.6→49.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.364 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. TWO SULFATE IONS COULD BE SOMETHING ELSE
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→49.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2410 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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