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- PDB-1t13: Crystal Structure Of Lumazine Synthase From Brucella Abortus Boun... -

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Basic information

Entry
Database: PDB / ID: 1t13
TitleCrystal Structure Of Lumazine Synthase From Brucella Abortus Bound To 5-nitro-6-(D-ribitylamino)-2,4(1H,3H) pyrimidinedione
Components6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
KeywordsTRANSFERASE
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
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-INI / PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase 2 / 6,7-dimethyl-8-ribityllumazine synthase 2
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKlinke, S. / Zylberman, V. / Vega, D.R. / Guimaraes, B.G. / Braden, B.C. / Goldbaum, F.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystallographic studies on Decameric Brucella spp. Lumazine Synthase: A Novel Quaternary Arrangement Evolved for a New Function?
Authors: Klinke, S. / Zylberman, V. / Vega, D.R. / Guimaraes, B.G. / Braden, B.C. / Goldbaum, F.A.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Aug 23, 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_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

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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)88,91615
Polymers86,9105
Non-polymers2,00610
Water1,60389
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

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)177,83130
Polymers173,81910
Non-polymers4,01220
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area36340 Å2
ΔGint-293 kcal/mol
Surface area45050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.321, 126.321, 165.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer of pentamers which can be generated applying crystallographic symmetry operations to the pentamer 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: 17381.900 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: RIBH, BMEII0589, BRA0695 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q44668, UniProt: P61711*PLUS, 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-INI / 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 306.229 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N4O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 4.2 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M Na MES pH=6.5, 0.1M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2003 / Details: Si single-crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2.9→52 Å / Num. obs: 34456 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4980 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DI0

1di0


Resolution: 2.9→52 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: The following residues were not located in the electronic density: Chain A: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Val157. Chain B: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Lys10, Thr11, ...Details: The following residues were not located in the electronic density: Chain A: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Val157. Chain B: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Lys10, Thr11, Leu156, Val157. Chain C: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Lys10, Thr11, Leu156, Val157. Chain D: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Lys10, Leu156, Val157. Chain E: Met3, Asn4, Gln5, Ser6, Cys7, Pro8, Asn9, Lys10, Leu156, Val157. The following residues present poor or missing side-chain electronic density and were modeled as alanine: Chain A: Arg152. Chain B: Glu121. Chain D: Thr11. Chain E: Thr11.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1706 -random
Rwork0.217 ---
all-34456 --
obs-34200 99.3 %-
Displacement parametersBiso mean: 41.5 Å2
Refinement stepCycle: LAST / Resolution: 2.9→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5739 0 130 89 5958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_deg1.4

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