+Open data
-Basic information
Entry | Database: PDB / ID: 4p77 | ||||||
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Title | Structure of ribB complexed with substrate Ru5P | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | LYASE / ribB / riboflvain / ligand / complex / crystal / Ru5P | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.04 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 | 4p77.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p77.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p77 ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p77 | HTTPS FTP |
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-Related structure data
Related structure data | 4p6cC 4p6dSC 4p6pC 4p8eC 4p8jC 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: Sugar | #3: Chemical | ChemComp-GOL / | #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: 2.05 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: Na2HPO4, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2010 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20 Å / Num. obs: 26194 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.04→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P6D Resolution: 2.04→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.839 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.175 / 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: 29.592 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→20 Å
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Refine LS restraints |
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