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- PDB-4kq6: Product complex of lumazine synthase from candida glabrata -

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Basic information

Entry
Database: PDB / ID: 4kq6
TitleProduct complex of lumazine synthase from candida glabrata
Components6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
KeywordsTRANSFERASE / Lumazine synthase / riboflavin 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
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-DLZ / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsShankar, M. / Wilbanks, S.M. / Nakatani, Y. / Monk, B.C. / Tyndall, J.D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata.
Authors: Shankar, M. / Wilbanks, S.M. / Nakatani, Y. / Monk, B.C. / Tyndall, J.D.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionMay 29, 2013ID: 4GEF
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 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_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

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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
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,16341
Polymers195,74410
Non-polymers3,41931
Water16,808933
1
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)99,43919
Polymers97,8725
Non-polymers1,56714
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-225 kcal/mol
Surface area30580 Å2
MethodPISA
2
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,72422
Polymers97,8725
Non-polymers1,85117
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-237 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.750, 84.840, 310.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.47316, 0.499138, 0.725934), (-0.842583, 0.497006, 0.207459), (-0.257243, -0.709821, 0.655729)-37.83131, -5.30299, 22.02592
3given(-0.380274, -0.03675, 0.924144), (-0.868733, -0.328636, -0.370542), (0.317324, -0.943742, 0.093045)-42.39365, 28.56392, 49.92488
4given(-0.381988, -0.870863, 0.309326), (-0.034244, -0.32114, -0.946412), (0.923532, -0.372111, 0.09285)-6.62513, 55.18514, 45.03174
5given(0.472952, -0.844751, -0.250425), (0.492725, 0.489203, -0.719654), (0.730437, 0.216971, 0.647599)18.81091, 37.59515, 14.55396
6given(-0.888727, 0.39884, 0.226032), (0.40544, 0.453689, 0.793589), (0.213967, 0.796927, -0.564912)-23.31214, -21.48448, 51.3648
7given(-0.069825, 0.99406, 0.083482), (0.994, 0.062269, 0.089928), (0.084196, 0.08926, -0.992443)-22.27127, 14.12078, 77.19202
8given(0.525847, 0.56336, -0.637268), (0.56423, -0.791679, -0.234283), (-0.636498, -0.236369, -0.734166)14.91858, 36.56578, 68.00951
9given(0.059127, -0.295814, -0.953414), (-0.296363, -0.917226, 0.266206), (-0.953243, 0.266817, -0.141901)36.70101, 14.45385, 36.4764
10given(-0.81679, -0.40475, -0.411136), (-0.390064, -0.137651, 0.910441), (-0.425094, 0.904008, -0.045446)13.07909, -21.62351, 26.40001

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase


Mass: 19574.422 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Strain: CBS-138 / Gene: CAGL0B01419g, RIB4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q6FXA8, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DLZ / 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol / 6,7-dimethyl-8-(1'-D-ribityl) lumazine / 6,7-Dimethyl-8-ribityllumazine


Mass: 326.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N4O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 933 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6 M AMMONIUM SULPHATE, 100 mM SODIUM, ACETATE AND 100 mM SODIUM CHLORIDE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2011 / Details: SILICON DOUBLE CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.24→47.43 Å / Num. obs: 105615 / Redundancy: 5.31 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EJB

1ejb


Resolution: 2.24→47.43 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.866 / SU B: 5.004 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25236 2012 1.9 %RANDOM
Rwork0.20034 ---
obs0.20137 101325 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2--1.11 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.24→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12179 0 196 933 13308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912554
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.97416957
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33251578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90225.038524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.634152250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.71560
X-RAY DIFFRACTIONr_chiral_restr0.1220.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219172
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.527 102 -
Rwork0.526 5255 -
obs--67.27 %

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