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- PDB-1nqw: Crystal Structure of Lumazine Synthase from Aquifex aeolicus in C... -

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Basic information

Entry
Database: PDB / ID: 1nqw
TitleCrystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / Lumazine synthase / Aquifex aeolicus / inhibitor complex / vitamin biosynthesis / catalytic mechanism
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 / 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-5YL / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, X. / Meining, W. / Cushman, M. / Haase, I. / Fischer, M. / Bacher, A. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus.
Authors: Zhang, X. / Meining, W. / Cushman, M. / Haase, I. / Fischer, M. / Bacher, A. / Ladenstein, R.
History
DepositionJan 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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: 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)85,69310
Polymers83,6365
Non-polymers2,0575
Water7,386410
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
x 12


Theoretical massNumber of molelcules
Total (without water)1,028,313120
Polymers1,003,63260
Non-polymers24,68160
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_766-z+2,-x+1,y+11
crystal symmetry operation8_746-z+2,x-1,-y+11
crystal symmetry operation9_645y+1,z-1,x1
crystal symmetry operation10_647-y+1,z-1,-x+21
crystal symmetry operation11_667y+1,-z+1,-x+21
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area318440 Å2
ΔGint-1546 kcal/mol
Surface area230780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)180.096, 180.096, 180.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1351-

HOH

21C-3351-

HOH

DetailsThe biological assembly is an icosahedral capsid generated from the pentamer in the asymmetric unit by the I23 crystllographic symmetry operactions

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Components

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


Mass: 16727.201 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-5YL / 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL) PENTYL-1-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.: 410 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 400, lithium sulphate, MOPS, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.5 mMEDTA1reservoir
30.5 mMsodium sulfite1reservoir
450 mMpotassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8482 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8482 Å / Relative weight: 1
ReflectionResolution: 2.2→48.13 Å / Num. all: 49207 / Num. obs: 49207 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / % possible all: 100
Reflection
*PLUS
Num. obs: 49238 / Num. measured all: 377239 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.13 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.177 2200 same indices as in the native data set. PDB ID: 1HQK
Rwork0.161 --
all0.161 49207 -
obs0.161 49207 -
Refinement stepCycle: LAST / Resolution: 2.2→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 135 410 6430
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.016
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.7
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg23.8
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg1.39

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