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- PDB-1ejb: LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1ejb
TitleLUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE
ComponentsLUMAZINE SYNTHASE
KeywordsTRANSFERASE / Lumazine synthase / Saccharomyces cerevisiae / X-ray structure analysis / Inhibitor complex / Vitamin biosynthesis
Function / homology
Function and homology information


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
Chem-INJ / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsMeining, W. / Mortl, S. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue.
Authors: Meining, W. / Mortl, S. / Fischer, M. / Cushman, M. / Bacher, A. / Ladenstein, R.
#1: Journal: J.Org.Chem. / Year: 1999
Title: Design and Biological Evaluation of Homologous Phosphonic Acids and Sulfonic Acids as Inhibitors of Lumazine Synthase
Authors: Cushman, M. / Mihalic, J.T. / Kis, K. / Bacher, A.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: LUMAZINE SYNTHASE
B: LUMAZINE SYNTHASE
C: LUMAZINE SYNTHASE
D: LUMAZINE SYNTHASE
E: LUMAZINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,29810
Polymers92,2425
Non-polymers2,0575
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-108 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.893, 82.893, 298.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
LUMAZINE SYNTHASE


Mass: 18448.316 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PNCO113 / Production host: Escherichia coli (E. coli)
References: UniProt: P50861, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-INJ / 5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID


Mass: 411.345 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H26N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium phosphate, potassium phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
21 Msodium potassium phosphate1drop
31.9 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.908
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 90091 / Num. obs: 89967 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 15.71 % / Biso Wilson estimate: 19.19 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 32
Reflection shellResolution: 1.85→1.87 Å / Rmerge(I) obs: 0.26 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 9999 Å / Observed criterion σ(I): 1 / Num. measured all: 510352
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 1.85→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4547 5 %Random
Rwork0.197 ---
all0.197 90091 --
obs0.197 89967 99.97 %-
Displacement parametersBiso mean: 22.094 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 135 550 7155
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d2.47
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.47
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.49
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg2.07

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