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- PDB-3wk1: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wk1 | ||||||
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Title | Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / protein-ligand complex / TIM barrel / decarboxylase / pyrimidine biosynthesis | ||||||
Function / homology | ![]() orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujihashi, M. / Pai, E.F. / Miki, K. | ||||||
![]() | ![]() Title: Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. Authors: Fujihashi, M. / Ishida, T. / Kuroda, S. / Kotra, L.P. / Pai, E.F. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wjwC ![]() 3wjxC ![]() 3wjyC ![]() 3wjzC ![]() 3wk0C ![]() 3wk2C ![]() 3wk3SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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
#1: Protein | Mass: 27379.402 Da / Num. of mol.: 1 / Mutation: L226R, N227I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: pyrF, MTH_129 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase | ||||
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#2: Chemical | ChemComp-O7E / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: Sodium citrate, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→51.78 Å / Num. obs: 30030 / % possible obs: 99.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.59→1.63 Å / Rmerge(I) obs: 0.298 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WK3 Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.593 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 70.41 Å2 / Biso mean: 14.0132 Å2 / Biso min: 2.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.595 Å / Origin y: 40.4939 Å / Origin z: 29.6907 Å
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Refinement TLS group |
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