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- PDB-2i0f: Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, ... -

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Basic information

Entry
Database: PDB / ID: 2i0f
TitleLumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)
Components6,7-dimethyl-8-ribityllumazine synthase 1Lumazine synthase
KeywordsTRANSFERASE / lumazine synthase RibH1
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
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
6,7-dimethyl-8-ribityllumazine synthase 1
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKlinke, S. / Zylberman, V. / Bonomi, H.R. / Haase, I. / Guimaraes, B.G. / Braden, B.C. / Bacher, A. / Fischer, M. / Goldbaum, F.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and Kinetic Properties of Lumazine Synthase Isoenzymes in the Order Rhizobiales
Authors: Klinke, S. / Zylberman, V. / Bonomi, H.R. / Haase, I. / Guimaraes, B.G. / Braden, B.C. / Bacher, A. / Fischer, M. / Goldbaum, F.A.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2013Group: Structure summary
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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 1
B: 6,7-dimethyl-8-ribityllumazine synthase 1
C: 6,7-dimethyl-8-ribityllumazine synthase 1
D: 6,7-dimethyl-8-ribityllumazine synthase 1
E: 6,7-dimethyl-8-ribityllumazine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,23910
Polymers84,0395
Non-polymers2005
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.101, 68.521, 90.649
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16807.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: ribH1, ribH, ribH-1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q57DY1, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 12% PEG 4000, 0.1M HEPES, 0.2M CALCIUM CHLORIDE, pH 7.7, 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: 1.438 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2005
RadiationMonochromator: SI SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. all: 35840 / Num. obs: 33602 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 43.06 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 12.3
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5150 / Rsym value: 0.282 / % possible all: 88.7

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F59

2f59


Resolution: 2.22→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1658 -RANDOM
Rwork0.2423 ---
obs0.2449 31466 92.4 %-
all-35840 --
Displacement parametersBiso mean: 44.27 Å2
Refinement stepCycle: LAST / Resolution: 2.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5479 0 5 181 5665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.149
X-RAY DIFFRACTIONc_bond_d0.0058

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