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- PDB-7uf3: RibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5... -

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Basic information

Entry
Database: PDB / ID: 7uf3
TitleRibB from Vibrio cholera bound with L-xylulose-5-phosphate (L-Xy5P) and manganese
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
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
: / L-xylulose-5-phosphate / 3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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)23,9855
Polymers23,5901
Non-polymers3954
Water2,198122
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)47,97010
Polymers47,1802
Non-polymers7908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3320 Å2
ΔGint-36 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.369, 79.016, 91.349
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-304-

MN

21A-442-

HOH

31A-512-

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-N3U / L-xylulose-5-phosphate


Type: L-saccharide / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
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→39.51 Å / Num. obs: 15092 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.26 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1060 / Rpim(I) all: 0.256

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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→39.51 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.1933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 1507 10 %
Rwork0.1612 13561 -
obs0.1665 15068 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.69 Å2
Refinement stepCycle: LAST / Resolution: 2→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 17 122 1770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081665
X-RAY DIFFRACTIONf_angle_d1.11672259
X-RAY DIFFRACTIONf_chiral_restr0.0548269
X-RAY DIFFRACTIONf_plane_restr0.0077300
X-RAY DIFFRACTIONf_dihedral_angle_d15.828626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.2491350.18111214X-RAY DIFFRACTION99.26
2.06-2.140.19771340.15851199X-RAY DIFFRACTION99.7
2.14-2.220.20291340.15121210X-RAY DIFFRACTION99.7
2.22-2.330.19951350.14611223X-RAY DIFFRACTION99.78
2.33-2.450.21311350.15721213X-RAY DIFFRACTION99.93
2.45-2.60.21231380.15761234X-RAY DIFFRACTION99.49
2.6-2.80.22851350.16581222X-RAY DIFFRACTION99.93
2.8-3.080.27491370.16231231X-RAY DIFFRACTION100
3.08-3.530.21351390.16841253X-RAY DIFFRACTION99.71
3.53-4.440.19791380.15431244X-RAY DIFFRACTION99.71
4.45-39.510.19621470.16691318X-RAY DIFFRACTION99.66

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