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- PDB-1tks: Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate Synthas... -

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Basic information

Entry
Database: PDB / ID: 1tks
TitleCrystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate Synthase of Candida albicans
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsISOMERASE / Candida albicans / riboflavin biosynthesis / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase / crystal structure synthetic gene
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 / mitochondrial intermembrane space / metal ion binding / cytosol
Similarity search - Function
3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / DHBP synthase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEcht, S. / Bauer, S. / Steinbacher, S. / Huber, R. / Bacher, A. / Fischer, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans.
Authors: Echt, S. / Bauer, S. / Steinbacher, S. / Huber, R. / Bacher, A. / Fischer, M.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-dihydroxy-2-butanone 4-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)45,3702
Polymers45,3702
Non-polymers00
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-19 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.439, 48.134, 59.804
Angle α, β, γ (deg.)66.229, 71.979, 89.856
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase


Mass: 22684.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / Gene: CARib3 / Plasmid: pNCO-CARib3-syn / Production host: Escherichia coli (E. coli) / Strain (production host): XL1
References: GenBank: 46438026, UniProt: Q5A3V6*PLUS, Isomerases; Intramolecular transferases; Transferring other groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Na-Citrat, PEG8000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 43264 / % possible obs: 84.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.7
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.221 / % possible all: 81.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G57

1g57


Resolution: 1.6→20 Å
RfactorNum. reflection
Rfree0.219 4367
Rwork0.192 -
obs-43263
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 0 676 3710
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection
Rfree0.219 4367
Rwork0.192 -
obs-43264

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