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- PDB-1tku: Crystal Structure of 3,4-Dihydroxy-2-butanone 4-phosphate Synthas... -

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Basic information

Entry
Database: PDB / ID: 1tku
TitleCrystal Structure of 3,4-Dihydroxy-2-butanone 4-phosphate Synthase of Candida albicans in complex with Ribulose-5-phosphate
Components3,4-Dihydroxy-2-butanone 4-phosphate Synthase
KeywordsISOMERASE / Candida albicans / riboflavin biosynthesis / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase / 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 / metal ion binding
Similarity search - Function
DHBP synthase / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / : / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8304
Polymers45,3702
Non-polymers4602
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-15 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.2, 47.9, 59.8
Angle α, β, γ (deg.)66.4, 72.3, 89.9
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: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Mes/NaOH, PEG8000, pH 6.0, 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 21, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 39461 / % possible obs: 77.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 22.2
Reflection shellResolution: 1.66→1.672 Å / Rmerge(I) obs: 0.174 / % possible all: 28.7

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Processing

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

1g57


Resolution: 1.66→20 Å
RfactorNum. reflection
Rfree0.218 3961
Rwork0.184 -
obs-39344
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 28 672 3734
LS refinement shellResolution: 1.66→1.72 Å
RfactorNum. reflection
Rfree0.218 3961
Rwork0.184 -
obs-39461

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