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

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Basic information

Entry
Database: PDB / ID: 4fxu
TitleCrystallographic structure of trimeric riboflavin synthase from Brucella abortus
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 / :
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 3, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)69,9613
Polymers69,9613
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-44 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.420, 93.480, 103.300
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 10% GLYCEROL, 0.5M 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: 1.9→50 Å / Num. all: 52161 / Num. obs: 52161 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 21.57
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 7.26 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.02 / Num. unique all: 8216 / Rsym value: 0.902 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4E0F

4e0f


Resolution: 1.9→27.72 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9215 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 2606 5 %RANDOM
Rwork0.2317 ---
obs0.2333 52107 99.94 %-
all-52107 --
Displacement parametersBiso mean: 50.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.1419 Å20 Å20 Å2
2---0.6431 Å20 Å2
3---3.7849 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 0 148 4291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014200HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145706HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1416SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes625HARMONIC5
X-RAY DIFFRACTIONt_it4200HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion18.81
X-RAY DIFFRACTIONt_chiral_improper_torsion583SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4658SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2663 190 5.02 %
Rwork0.2396 3594 -
all0.2409 3784 -
obs--99.94 %

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