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- PDB-2f59: Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, ... -

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Basic information

Entry
Database: PDB / ID: 2f59
TitleLumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione
Components6,7-dimethyl-8-ribityllumazine synthase 1Lumazine synthase
KeywordsTRANSFERASE / Enzyme-substrate analogue / inhibitor complex
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
Chem-INI / 6,7-dimethyl-8-ribityllumazine synthase 1
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)85,81016
Polymers84,0395
Non-polymers1,77211
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-103 kcal/mol
Surface area25010 Å2
MethodPISA, PQS
2
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

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)171,62132
Polymers168,07710
Non-polymers3,54322
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_644y+1,x-1,-z-11
Buried area27660 Å2
ΔGint-271 kcal/mol
Surface area48310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.317, 95.317, 171.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-303-

CA

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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.: 6 / Source method: obtained synthetically / Formula: Ca
#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.: 219 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 292 K / pH: 6.6
Details: 18% PEG 400, 0.1M MES, 0.2M calcium chloride, pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 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: 2.3→33.5 Å / Num. obs: 40642 / % possible obs: 99.5 % / Redundancy: 9.5 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.49
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.34 / % possible all: 97

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RVV, STARTING RESIDUE 49

1rvv


Resolution: 2.3→33.5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2011 -RANDOM
Rwork0.217 ---
obs0.217 40562 99.2 %-
all-40874 --
Displacement parametersBiso mean: 34.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 111 219 5793
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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