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- PDB-1i8d: CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1i8d
TitleCRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE
ComponentsRIBOFLAVIN SYNTHASE
KeywordsTRANSFERASE / riboflavin synthase / riboflavin biosynthesis / antimicrobial target / structure-based design / Escherichia coli
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / cytosol
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Riboflavin synthase-like beta-barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Riboflavin synthase / Riboflavin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLiao, D.-I. / Wawrzak, Z. / Calabrese, J.C. / Viitanen, P.V. / Jordan, D.B.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of riboflavin synthase.
Authors: Liao, D.I. / Wawrzak, Z. / Calabrese, J.C. / Viitanen, P.V. / Jordan, D.B.
History
DepositionMar 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOFLAVIN SYNTHASE
B: RIBOFLAVIN SYNTHASE
C: RIBOFLAVIN SYNTHASE


Theoretical massNumber of molelcules
Total (without water)70,4193
Polymers70,4193
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-41 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.083, 61.705, 219.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homo trimer. The three molecules in the asymmetric unit represent the biological assembly. The trimer is asymmetrical.

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Components

#1: Protein RIBOFLAVIN SYNTHASE


Mass: 23472.885 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BACTERIA / Plasmid: PET-24A(+) (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P29015, UniProt: P0AFU8*PLUS, riboflavin synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: bis-tris propane, MgCl2, diglyme, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1dropor Se-Met-labeled RS
250 mMTris-HCl1drop
37-10 %diglyme1reservoir
425 mMBis-Tris propane-NaOH1reservoir
520-50 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.1271 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 48686 / Num. obs: 437196 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.7
Reflection shellResolution: 2→2.04 Å / Redundancy: 5 % / Rmerge(I) obs: 0.215 / % possible all: 96.7
Reflection
*PLUS
Num. obs: 48686 / Num. measured all: 437196
Reflection shell
*PLUS
% possible obs: 96.7 % / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
SHARPphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→25 Å / σ(F): 2 / Stereochemistry target values: TNT library
RfactorNum. reflection
Rfree0.299 2400
Rwork0.239 -
all-48686
obs-48007
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 0 229 4807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.99
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.99

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