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- PDB-1vqt: Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vqt | ||||||
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Title | Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution | ||||||
![]() | Orotidine 5'-phosphate decarboxylase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 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 | ![]() | 53.9 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1eixS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 24307.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9WYG7, ![]() | ||
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#2: Chemical | ChemComp-EDO / ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.04 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5 Details: 12.0% PEG-20000, 0.1M MES pH 6.5, 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: Sep 30, 2004 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→99 Å / Num. obs: 17410 / % possible obs: 99.47 % / Redundancy: 4.81 % / Biso Wilson estimate: 55.68 Å2 / Rsym value: 0.066 / Net I/σ(I): 28.05 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.41 % / Mean I/σ(I) obs: 1.34 / Num. unique all: 836 / % possible all: 95.32 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1EIX Resolution: 2→27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 10.256 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.589 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.8629 Å / Origin y: -0.5404 Å / Origin z: 6.3329 Å
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Refinement TLS group | Selection: ALL |