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- PDB-1kyv: Lumazine Synthase from S.pombe bound to riboflavin -

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Basic information

Entry
Database: PDB / ID: 1kyv
TitleLumazine Synthase from S.pombe bound to riboflavin
Components6,7-Dimethyl-8-ribityllumazine Synthase
KeywordsTRANSFERASE / riboflavin biosynthesis / lumazine synthase / Schizosaccharomyces pombe / ligand binding
Function / homology
Function and homology information


riboflavin synthase activity / riboflavin binding / 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / mitochondrial intermembrane space / nucleus / cytoplasm
Similarity search - Function
Lumazine/riboflavin synthase / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / RIBOFLAVIN / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGerhardt, S. / Haase, I. / Steinbacher, S. / Kaiser, J.T. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.
Authors: Gerhardt, S. / Haase, I. / Steinbacher, S. / Kaiser, J.T. / Cushman, M. / Bacher, A. / Huber, R. / Fischer, M.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 23, 2013Group: Structure summary
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 6,7-Dimethyl-8-ribityllumazine Synthase
B: 6,7-Dimethyl-8-ribityllumazine Synthase
C: 6,7-Dimethyl-8-ribityllumazine Synthase
D: 6,7-Dimethyl-8-ribityllumazine Synthase
E: 6,7-Dimethyl-8-ribityllumazine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,39115
Polymers86,0345
Non-polymers2,35710
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17230 Å2
ΔGint-110 kcal/mol
Surface area25920 Å2
MethodPISA
2
A: 6,7-Dimethyl-8-ribityllumazine Synthase
B: 6,7-Dimethyl-8-ribityllumazine Synthase
C: 6,7-Dimethyl-8-ribityllumazine Synthase
D: 6,7-Dimethyl-8-ribityllumazine Synthase
E: 6,7-Dimethyl-8-ribityllumazine Synthase
hetero molecules

A: 6,7-Dimethyl-8-ribityllumazine Synthase
B: 6,7-Dimethyl-8-ribityllumazine Synthase
C: 6,7-Dimethyl-8-ribityllumazine Synthase
D: 6,7-Dimethyl-8-ribityllumazine Synthase
E: 6,7-Dimethyl-8-ribityllumazine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,78130
Polymers172,06810
Non-polymers4,71320
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area37470 Å2
ΔGint-228 kcal/mol
Surface area48830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.500, 145.523, 128.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
6,7-Dimethyl-8-ribityllumazine Synthase


Mass: 17206.791 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pNCO113 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UUB1, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H20N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: citrate, sodium formate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlenzyme1drop
220 mMpotassium phosphate1droppH7.0
350 mM1dropKCl
40.1 Mcitrate1reservoirpH4.9-5.2
51.5 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→16.03 Å / Num. all: 41051 / Num. obs: 40966 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.53 Å / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→16.03 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2128 4118 RANDOM
Rwork0.1801 --
all0.189 41051 -
obs0.189 40966 -
Refinement stepCycle: LAST / Resolution: 2.4→16.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5645 0 160 94 5899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.012104
X-RAY DIFFRACTIONc_angle_deg1.75186
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.189 / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.75

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