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- PDB-4g6i: Crystallographic structure of trimeric riboflavin synthase from B... -

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Basic information

Entry
Database: PDB / ID: 4g6i
TitleCrystallographic structure of trimeric riboflavin synthase from Brucella abortus in complex with roseoflavin
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 / Chem-RS3 / :
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 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)71,5837
Polymers69,9613
Non-polymers1,6224
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-44 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.040, 92.570, 102.580
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-RS3 / 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol / Roseoflavin


Mass: 405.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 10% GLYCEROL, 0.5 M POTASSIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 60197 / Num. obs: 60197 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.96 % / Biso Wilson estimate: 34.63 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 21.24
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 2.97 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9547 / Rsym value: 0.514 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4E0F

4e0f


Resolution: 1.78→32.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.824 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27278 3010 5 %RANDOM
Rwork0.23987 ---
all0.2415 60193 --
obs0.2415 60193 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.78→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 116 240 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194754
X-RAY DIFFRACTIONr_angle_refined_deg0.9451.9886463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5675594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57224.098205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1811537
X-RAY DIFFRACTIONr_chiral_restr0.0590.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213541
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 204 -
Rwork0.342 3912 -
obs-4116 95.3 %

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