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- PDB-7uf0: RibB from Vibrio cholera bound with D-ribulose-5-phosphate (D-Ru5P) -

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Basic information

Entry
Database: PDB / ID: 7uf0
TitleRibB from Vibrio cholera bound with D-ribulose-5-phosphate (D-Ru5P)
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / RibB / riboflavin / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase RibB-like alpha/beta domain superfamily
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKenjic, N. / Meneely, K.M. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1904494 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis.
Authors: Kenjic, N. / Meneely, K.M. / Wherritt, D.J. / Denler, M.C. / Jackson, T.A. / Moran, G.R. / Lamb, A.L.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8202
Polymers23,5901
Non-polymers2301
Water2,666148
1
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules

A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6404
Polymers47,1802
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3980 Å2
ΔGint-16 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.671, 78.625, 90.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21A-537-

HOH

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 23589.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ribB, D6U24_02240, ERS013198_00268, ERS013199_01247, ERS013202_00910, ERS013207_00669, FXE67_08125
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H6NPW4, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M lithium acetate, 12-18% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→39.31 Å / Num. obs: 20407 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.78 Å2 / Rpim(I) all: 0.048 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1209 / Rpim(I) all: 0.359

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4P8E

4p8e


Resolution: 1.8→39.31 Å / SU ML: 0.1779 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2019 2000 9.82 %
Rwork0.1654 18375 -
obs0.169 20375 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 14 148 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111685
X-RAY DIFFRACTIONf_angle_d1.23712289
X-RAY DIFFRACTIONf_chiral_restr0.0557272
X-RAY DIFFRACTIONf_plane_restr0.0096305
X-RAY DIFFRACTIONf_dihedral_angle_d15.4438636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.2921440.23211313X-RAY DIFFRACTION99.45
1.84-1.890.26771380.19731281X-RAY DIFFRACTION99.86
1.89-1.950.24831390.1771277X-RAY DIFFRACTION99.86
1.95-2.010.23671410.17651291X-RAY DIFFRACTION99.72
2.01-2.080.22881400.1861290X-RAY DIFFRACTION99.86
2.09-2.170.24261430.16791316X-RAY DIFFRACTION99.86
2.17-2.270.19651410.15861294X-RAY DIFFRACTION99.93
2.27-2.390.2361420.15691305X-RAY DIFFRACTION99.93
2.39-2.540.19121430.15961307X-RAY DIFFRACTION99.93
2.54-2.730.21861420.16971310X-RAY DIFFRACTION99.79
2.73-3.010.21331430.17251316X-RAY DIFFRACTION100
3.01-3.440.20091450.16921326X-RAY DIFFRACTION100
3.44-4.330.17471460.14911352X-RAY DIFFRACTION100
4.34-39.310.15941530.15721397X-RAY DIFFRACTION99.74

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