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- PDB-1di0: CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS -

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Basic information

Entry
Database: PDB / ID: 1di0
TitleCRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS
ComponentsLUMAZINE 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 / 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
PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase 2
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsBraden, B.C. / Velikovsky, C.A. / Cauerhff, A.A. / Polikarpov, I. / Goldbaum, F.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Divergence in macromolecular assembly: X-ray crystallographic structure analysis of lumazine synthase from Brucella abortus.
Authors: Braden, B.C. / Velikovsky, C.A. / Cauerhff, A.A. / Polikarpov, I. / Goldbaum, F.A.
#1: Journal: J.Struct.Biol. / Year: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Lumazine Synthase from Brucella abortus
Authors: Goldbaum, F.A. / Polikarpov, I. / Cauerhff, A.A. / Velikovsky, C.A. / Braden, B.C. / Poljak, R.J.
History
DepositionNov 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)87,93418
Polymers86,6995
Non-polymers1,23513
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15470 Å2
ΔGint-184 kcal/mol
Surface area27220 Å2
MethodPISA
2
A: LUMAZINE SYNTHASE
B: LUMAZINE SYNTHASE
C: LUMAZINE SYNTHASE
D: LUMAZINE SYNTHASE
E: LUMAZINE SYNTHASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)175,86736
Polymers173,39810
Non-polymers2,46926
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area38780 Å2
ΔGint-437 kcal/mol
Surface area46610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.250, 142.250, 242.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsPentameric assembly of lumazine synthase monomers.

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Components

#1: Protein
LUMAZINE SYNTHASE


Mass: 17339.795 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P61711
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M ammonium sulfate, 0.1M phoshate buffer, pH 5, VAPOR DIFFUSION, HANGING DROP
Temp details: ambient
Crystal grow
*PLUS
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.25 Mammonium sulfate1reservoir
20.1 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. all: 26193 / Num. obs: 20404 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.7→150 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.23 1998 -
Rwork0.18 --
all0.18 --
obs0.18 20404 90 %
Refinement stepCycle: LAST / Resolution: 2.7→150 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 65 47 5818
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 150 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg2.56
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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