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- PDB-7vm0: Crystal structure of YojK from B.subtilis in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 7vm0
TitleCrystal structure of YojK from B.subtilis in complex with UDP
ComponentsGlycosyl transferase family 1
KeywordsTRANSFERASE / complex / dimer
Function / homologyUDP-glycosyltransferase, MGT-like / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / hexosyltransferase activity / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHou, X.D. / Guo, B.D. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2018YFA0901700 China
Other privateJUSRP12015 China
Other private2020M671329 China
Other private2020Z383 China
CitationJournal: Front Bioeng Biotechnol / Year: 2022
Title: Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK.
Authors: Guo, B. / Hou, X. / Zhang, Y. / Deng, Z. / Ping, Q. / Fu, K. / Yuan, Z. / Rao, Y.
History
DepositionOct 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 19, 2022Group: Advisory / Database references ...Advisory / Database references / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num
Revision 2.1Nov 29, 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: Glycosyl transferase family 1
B: Glycosyl transferase family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8078
Polymers93,6002
Non-polymers1,2076
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-28 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.602, 81.053, 100.676
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyl transferase family 1 / Glycosyltransferase / Macrolide glycosyltransferase


Mass: 46799.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yojK1, B4417_0117, CFD21_20150 / Production host: Escherichia coli (E. coli) / References: UniProt: L7V2W3
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.09 M magnesium chloride, 0.09 M Tris-HCl, pH8.0, 25.2% (w/v) PEG3,350 and 0.05M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 58223 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 0.955 / Net I/σ(I): 6 / Num. measured all: 401222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9370.5329110.8980.2150.5730.88699.5
1.93-1.977.10.47428910.9080.1920.5120.94499.2
1.97-2.0170.4129210.9240.1660.4430.94399.5
2.01-2.0570.35828940.9370.1450.3870.96299.3
2.05-2.0970.30829240.950.1250.3330.99699.2
2.09-2.1470.25928970.9620.1050.280.98798.9
2.14-2.196.90.2329120.9690.0940.2490.99698.9
2.19-2.256.90.20128670.9760.0820.2181.00398.7
2.25-2.326.70.1829300.980.0750.1951.00298.8
2.32-2.396.10.15128190.980.0660.1651.00896.3
2.39-2.4870.14329150.9860.0580.1551.00999.5
2.48-2.587.20.13229550.9870.0530.1421.01499.9
2.58-2.77.10.11429190.990.0460.1230.99899.8
2.7-2.847.10.10129130.990.0410.1090.99199.4
2.84-3.0270.08829280.9920.0360.0950.9698.6
3.02-3.256.80.07928860.9920.0330.0860.93298.5
3.25-3.586.30.06928830.9940.0290.0750.92696.8
3.58-4.097.20.06329340.9950.0260.0680.9299.6
4.09-5.1670.05929690.9940.0240.0640.85699.5
5.16-506.40.05629550.9960.0240.0610.75597.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMAC5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KQX
Resolution: 1.9→42.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.87 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2799 4.8 %RANDOM
Rwork0.1977 ---
obs0.1999 55196 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.69 Å2 / Biso mean: 22.986 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.17 Å2
2---0.05 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.9→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 76 173 6527
Biso mean--20.56 20.24 -
Num. residues----792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175963
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6538738
X-RAY DIFFRACTIONr_angle_other_deg1.3721.58213905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9324.332337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.949151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4711522
X-RAY DIFFRACTIONr_chiral_restr0.0860.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021306
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 177 -
Rwork0.248 3884 -
all-4061 -
obs--93.59 %

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