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- PDB-2zz1: Snapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zz1 | ||||||
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Title | Snapshot of the reaction from 6-CN-UMP to BMP catalyzed by Orotidine Monophosphate Deacarboxylase from M. thermoautotrophicum | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ODCASE) / BARBITURIC ACID RIBOSYL 5'-MONOPHOSPHATE (BMP) / 6-CYANOUMP OMP decarboxylase / OMPDC / OMPDCASE / 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. | ||||||
![]() | ![]() Title: Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase Authors: Fujihashi, M. / Wei, L. / Kotra, L.P. / Pai, E.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 82.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zz2C ![]() 2zz3C ![]() 2zz4C ![]() 2zz5C ![]() 2zz6C ![]() 2zz7C ![]() 1x1zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 27379.402 Da / Num. of mol.: 2 / Mutation: R226L,I227N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET15B / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | BMP 301(302) AND 6CN 303(304) ARE IN ALTERNATE CONFORMATI | Sequence details | ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow | Method: vapor diffusion Details: 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION PH range: 6.0-8.5 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003 / Details: default |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→100 Å / Num. obs: 60802 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.57→1.6 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.296 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1x1z Resolution: 1.57→51.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.465 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.243 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→51.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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