+Open data
-Basic information
Entry | Database: PDB / ID: 4p6d | ||||||
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Title | Structure of ribB complexed with PO4 ion | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / ribB / riboflavin / ligand / complex / crystal | ||||||
Function / homology | Function and homology information 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 | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Islam, Z. / Kumar, A. / Singh, S. / Salmon, L. / Karthikeyan, S. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p6d.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p6d.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 4p6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p6d ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p6d | HTTPS FTP |
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-Related structure data
Related structure data | 4p6cC 4p6pC 4p77C 4p8eC 4p8jC 1g57S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: ribB, VC_A1060 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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