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- PDB-4e0f: Crystallographic structure of trimeric Riboflavin Synthase from B... -

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Basic information

Entry
Database: PDB / ID: 4e0f
TitleCrystallographic structure of trimeric Riboflavin Synthase from Brucella abortus in complex with riboflavin
ComponentsRiboflavin synthase subunit alpha
KeywordsTRANSFERASE / beta barrel / alpha + beta protein / Riboflavin biosynthesis
Function / homologyElongation Factor Tu (Ef-tu); domain 3 - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / RIBOFLAVIN / :
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSerer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic and kinetic study of riboflavin synthase from Brucella abortus, a chemotherapeutic target with an enhanced intrinsic flexibility.
Authors: Serer, M.I. / Bonomi, H.R. / Guimaraes, B.G. / Rossi, R.C. / Goldbaum, F.A. / Klinke, S.
History
DepositionMar 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Structure summary
Revision 1.2May 14, 2014Group: Database references
Revision 1.3May 28, 2014Group: Database references
Revision 1.4Sep 13, 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_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: Riboflavin synthase subunit alpha
B: Riboflavin synthase subunit alpha
C: Riboflavin synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3374
Polymers69,9613
Non-polymers3761
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-47 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.98, 91.82, 98.77
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Riboflavin synthase subunit alpha /


Mass: 23320.361 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: ribE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G8SX20, riboflavin synthase
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 8000, 10% Glycerol, 0.5M Potassium Chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2011 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→67.25 Å / Num. all: 15167 / Num. obs: 15167 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 5.9
Reflection shellResolution: 2.85→3 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2177 / Rsym value: 0.385 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Blu-Ice/ DCSdata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Monomer from PDB entry 1I8D

1i8d


Resolution: 2.85→67.25 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.829 / SU B: 16.354 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26705 751 5 %RANDOM
Rwork0.21565 ---
all0.21812 14375 --
obs0.21812 14375 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.82 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.85→67.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 27 66 4683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224700
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9636385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.465604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53724.098205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27115777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9021536
X-RAY DIFFRACTIONr_chiral_restr0.060.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213529
X-RAY DIFFRACTIONr_mcbond_it0.2251.52986
X-RAY DIFFRACTIONr_mcangle_it0.42624767
X-RAY DIFFRACTIONr_scbond_it0.48131714
X-RAY DIFFRACTIONr_scangle_it0.884.51617
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 51 -
Rwork0.276 1044 -
obs--98.21 %

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