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

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Basic information

Entry
Database: PDB / ID: 4gqn
TitleCrystallographic structure of trimeric Riboflavin Synthase from Brucella abortus in complex with 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione
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-INI / :
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionAug 23, 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)71,7989
Polymers69,9613
Non-polymers1,8376
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-44 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.850, 92.300, 99.090
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: BAA13334_I02741, RIBE / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G8SX20, riboflavin synthase
#2: Chemical
ChemComp-INI / 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE


Mass: 306.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 8000, 10% GLYCEROL, 0.5 M 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 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: 1.85→50 Å / Num. all: 55235 / Num. obs: 55235 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.81 % / Biso Wilson estimate: 28.68 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 15.65
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.99 / Num. unique all: 8736 / Rsym value: 0.773 / % 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: 1.85→27.09 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9237 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 2765 5.01 %RANDOM
Rwork0.1999 ---
all0.2016 55210 --
obs0.2016 55210 99.73 %-
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.1766 Å20 Å20 Å2
2---3.5759 Å20 Å2
3----1.6007 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 1.85→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 126 307 5070
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074836HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996558HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1698SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes766HARMONIC5
X-RAY DIFFRACTIONt_it4836HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion17.12
X-RAY DIFFRACTIONt_chiral_improper_torsion644SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5608SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2298 201 5.05 %
Rwork0.2169 3780 -
all0.2175 3981 -
obs-3981 99.73 %

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