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- PDB-2obx: Lumazine synthase RibH2 from Mesorhizobium loti (Gene mll7281, Sw... -

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Basic information

Entry
Database: PDB / ID: 2obx
TitleLumazine synthase RibH2 from Mesorhizobium loti (Gene mll7281, Swiss-Prot entry Q986N2) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione
Components6,7-dimethyl-8-ribityllumazine synthase 1
KeywordsTRANSFERASE / lumazine synthase / alpha-beta
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
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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 / 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 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
F: 6,7-dimethyl-8-ribityllumazine synthase 1
G: 6,7-dimethyl-8-ribityllumazine synthase 1
H: 6,7-dimethyl-8-ribityllumazine synthase 1
I: 6,7-dimethyl-8-ribityllumazine synthase 1
J: 6,7-dimethyl-8-ribityllumazine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,96329
Polymers173,04610
Non-polymers3,91719
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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


Theoretical massNumber of molelcules
Total (without water)88,43414
Polymers86,5235
Non-polymers1,9119
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-135 kcal/mol
Surface area27300 Å2
MethodPISA
3
F: 6,7-dimethyl-8-ribityllumazine synthase 1
G: 6,7-dimethyl-8-ribityllumazine synthase 1
H: 6,7-dimethyl-8-ribityllumazine synthase 1
I: 6,7-dimethyl-8-ribityllumazine synthase 1
J: 6,7-dimethyl-8-ribityllumazine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,52915
Polymers86,5235
Non-polymers2,00610
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-134 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.385, 122.218, 94.929
Angle α, β, γ (deg.)90.00, 125.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11J-1009-

PO4

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Components

#1: Protein
6,7-dimethyl-8-ribityllumazine synthase 1 / E.C.2.5.1.9 / DMRL synthase 1 / Lumazine synthase 1 / Riboflavin synthase 1 beta chain


Mass: 17304.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: ribH1, ribH / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q986N2, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / 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.: 10 / Source method: obtained synthetically / Formula: C9H14N4O8
#4: Water ChemComp-HOH / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 16% PEG 4000, 15% isopropanol, 20mM sodium/potassium phosphate pH 7.0, 0.1M ammonium sulfate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 26, 2006
RadiationMonochromator: SI double crystal monocromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.53→87.7 Å / Num. all: 46427 / Num. obs: 46427 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 9.7
Reflection shellResolution: 2.53→2.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6236 / Rsym value: 0.255 / % possible all: 89.2

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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 1T13

1t13


Resolution: 2.53→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2805 2329 -random
Rwork0.2131 ---
obs0.2165 46386 96.6 %-
all-48011 --
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 2.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11219 0 255 219 11693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_deg1.413

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