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- PDB-3ez4: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransfe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ez4 | ||||||
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Title | Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei | ||||||
![]() | 3-methyl-2-oxobutanoate hydroxymethyltransferase | ||||||
![]() | TRANSFERASE / Cytoplasm / Magnesium / Metal-binding / Methyltransferase / Pantothenate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | ![]() 3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei Authors: Edwards, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 471.4 KB | Display | ![]() |
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PDB format | ![]() | 385.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m3uS 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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Components
#1: Protein | Mass: 28542.816 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q63R49, UniProt: Q3JP15*PLUS, 3-methyl-2-oxobutanoate hydroxymethyltransferase #2: Chemical | ChemComp-TRS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PACT screen condition H11, 0.1 M BisTris propane, 20% PEG 3350, 0.2 M Na Citrate, 0.4/0.4 uL drops, 24.4 mg/mL protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 157415 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Χ2: 0.924 / Net I/σ(I): 13.461 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.3 / Num. unique all: 15125 / Χ2: 0.483 / % possible all: 96 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1M3U Resolution: 2.1→38.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.831 / SU B: 4.585 / SU ML: 0.121 / SU R Cruickshank DPI: 0.218 / SU Rfree: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.188 / 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 max: 60.39 Å2 / Biso mean: 23.973 Å2 / Biso min: 5.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.152 Å / Total num. of bins used: 20
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