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- PDB-7uf4: RibB from Vibrio cholera bound with intermediate 1 of the reactio... -

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Basic information

Entry
Database: PDB / ID: 7uf4
TitleRibB from Vibrio cholera bound with intermediate 1 of the reaction cycle and 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 / : / Chem-N46 / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)24,3288
Polymers23,5901
Non-polymers7387
Water93752
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)48,65616
Polymers47,1802
Non-polymers1,47714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5120 Å2
ΔGint-33 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.337, 78.558, 90.535
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-403-

HOH

21A-417-

HOH

31A-452-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#3: 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

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Non-polymers , 4 types, 58 molecules

#2: Chemical ChemComp-N46 / (2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate


Mass: 212.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.91 %
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: 2.2→39.28 Å / Num. obs: 11272 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.41 Å2 / Rpim(I) all: 0.059 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 955 / Rpim(I) all: 0.341

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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: 2.2→39.28 Å / SU ML: 0.2633 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 1125 10 %
Rwork0.1688 10124 -
obs0.1744 11249 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 41 52 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181686
X-RAY DIFFRACTIONf_angle_d1.32492282
X-RAY DIFFRACTIONf_chiral_restr0.0597270
X-RAY DIFFRACTIONf_plane_restr0.0135302
X-RAY DIFFRACTIONf_dihedral_angle_d7.5489237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.29651380.20341237X-RAY DIFFRACTION99.42
2.3-2.420.28141360.18941236X-RAY DIFFRACTION99.78
2.42-2.570.23991390.18551251X-RAY DIFFRACTION99.93
2.57-2.770.26241390.19251259X-RAY DIFFRACTION100
2.77-3.050.25031400.18311251X-RAY DIFFRACTION99.86
3.05-3.490.23561400.1751260X-RAY DIFFRACTION100
3.49-4.390.20511420.15061283X-RAY DIFFRACTION99.86
4.4-39.280.18181510.15121347X-RAY DIFFRACTION99.87

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