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- PDB-3m44: Crystal structure of the mutant V201A of orotidine 5'-monophospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m44 | ||||||
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Title | Crystal structure of the mutant V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / orotidine 5'-monophosphate decarboxylase / mutant V201A | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation. Authors: Wood, B.M. / Amyes, T.L. / Fedorov, A.A. / Fedorov, E.V. / Shabila, A. / Almo, S.C. / Richard, J.P. / Gerlt, J.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 | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 74.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lhtC ![]() 3lhuC ![]() 3lhvC ![]() 3lhwC ![]() 3lhyC ![]() 3lhzC ![]() 3li1C ![]() 3lldC ![]() 3llfC ![]() 3ltpC ![]() 3ltsC ![]() 3ltyC ![]() 3lv5C ![]() 3lv6C ![]() 3m1zC ![]() 3m41C ![]() 3m43C ![]() 3m47C ![]() 3m5xC ![]() 3m5yC ![]() 3m5zC ![]() 3g18S 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: 24856.645 Da / Num. of mol.: 2 / Mutation: V201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pyrF, MTH_129 / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 4, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33.76 Å / Num. all: 73236 / Num. obs: 73236 / % possible obs: 90.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3G18 Resolution: 1.4→33.76 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.914 Å2 / ksol: 0.436 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→33.76 Å
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Refine LS restraints |
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LS refinement shell |
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