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Open data
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Basic information
Entry | Database: PDB / ID: 4p6d | ||||||
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Title | Structure of ribB complexed with PO4 ion | ||||||
![]() | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
![]() | LYASE / ribB / riboflavin / ligand / complex / crystal | ||||||
Function / homology | ![]() GTP cyclohydrolase II activity / 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Islam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae. Authors: Islam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.4 KB | Display | ![]() |
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PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p6cC ![]() 4p6pC ![]() 4p77C ![]() 4p8eC ![]() 4p8jC ![]() 1g57S 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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Unit cell |
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Components
#1: Protein | Mass: 25674.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9KKP2, 3,4-dihydroxy-2-butanone-4-phosphate synthase #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.2 % / Description: rod shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: NaH2PO4, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2009 / Details: MIRROR |
Radiation | Monochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→20 Å / Num. obs: 52849 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 11.92 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 7.4 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G57 Resolution: 1.59→19.436 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.46 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→19.436 Å
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Refine LS restraints |
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LS refinement shell |
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