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- PDB-1xn1: Crystal Structure Of Lumazine Synthase From Brucella Abortus (Ort... -

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Basic information

Entry
Database: PDB / ID: 1xn1
TitleCrystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)
Components6,7-dimethyl-8-ribityllumazine 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
PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase 2
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 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 1.4Aug 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
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)177,70056
Polymers173,81910
Non-polymers3,88146
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.554, 120.238, 159.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL ASSEMBLY ARE DIMERS OF PENTAMERS WHICH CAN BE OBTAINED APPLYING THE FOLLOWING OPERATIONS: TO CHAINS A,B,C,D,E: (1/2+X,3/2-Y,1-Z) ; TO CHAINS F,G,H,I,J: (-1/2+X,3/2-Y,1-Z)

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Components

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


Mass: 17381.900 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: ribH / Plasmid: PET11B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P61711, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.3M AMMONIUM SULFATE, 0.1M NA MES, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2004 / Details: SI SINGLE CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 3.05→56 Å / Num. all: 43004 / Num. obs: 43004 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 49.56 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 5.8
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6168 / Rsym value: 0.331 / % possible all: 98.8

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Processing

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

1di0


Resolution: 3.05→56 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2088 -RANDOM
Rwork0.199 ---
obs0.202 42320 97.6 %-
all-42920 --
Displacement parametersBiso mean: 23.53 Å2
Refinement stepCycle: LAST / Resolution: 3.05→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11360 0 202 16 11578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_angle_deg1.608

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