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- PDB-2a59: Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizos... -

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Basic information

Entry
Database: PDB / ID: 2a59
TitleStructure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound ligand 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
Components6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
KeywordsTRANSFERASE / 6 / 7-Dimethyl-8-ribityllumazine synthase / Schizosaccharomyces pombe / mutant W27Y / LUSY / 5-nitroso-6-ribitylamino-2 / 4(1H / 3H)-pyrimidinedione
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 / cytosol / 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-LMZ / PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsKoch, M. / Breithaupt, C. / Gerhardt, S. / Haase, I. / Weber, S. / Cushman, M. / Huber, R. / Bacher, A. / Fischer, M.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase
Authors: Koch, M. / Breithaupt, C. / Gerhardt, S. / Haase, I. / Weber, S. / Cushman, M. / Huber, R. / Bacher, A. / Fischer, M.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)87,84515
Polymers85,9195
Non-polymers1,92610
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-90 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.150, 144.810, 127.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthe biological assembly is the pentamer found in the asymmetric unit

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase / DMRL synthase / Lumazine synthase / Riboflavin synthase beta chain


Mass: 17183.756 Da / Num. of mol.: 5 / Mutation: W27Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: rib4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UUB1, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-LMZ / 5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 290.230 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N4O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: sodium citrate, ammonium dihydrogen phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 28707 / Num. obs: 28707 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.026 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1393 4.9 %RANDOM
Rwork0.191 ---
all0.191 28707 --
obs0.191 28599 99.8 %-
Solvent computationBsol: 32.822 Å2
Displacement parametersBiso mean: 44.287 Å2
Baniso -1Baniso -2Baniso -3
1-3.038 Å20 Å20 Å2
2--1.395 Å20 Å2
3----4.432 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 125 58 5728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.42
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2no.par
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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