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- PDB-7vlb: Crystal structure of UGT109A1 from Bacillus -

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Basic information

Entry
Database: PDB / ID: 7vlb
TitleCrystal structure of UGT109A1 from Bacillus
ComponentsUDP-glycosyltransferase
KeywordsTRANSFERASE / glycosyl transferase / UGT109A1
Function / homologyUDP-glycosyltransferase, MGT-like / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glycosyltransferase activity / UDP-glucuronosyl/UDP-glucosyltransferase / hexosyltransferase activity / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase
Function and homology information
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, L.Q. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of UGT109A1 from Bacillus
Authors: Chen, L.Q. / Zhang, Y.
History
DepositionOct 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase
B: UDP-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4674
Polymers87,6582
Non-polymers8082
Water39622
1
A: UDP-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2332
Polymers43,8291
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area17020 Å2
MethodPISA
2
B: UDP-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2332
Polymers43,8291
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-10 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.874, 137.874, 135.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UDP-glycosyltransferase


Mass: 43829.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A289QH46
#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 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 3→48.75 Å / Num. obs: 26821 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.618 / Num. unique obs: 1302 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IIR
Resolution: 3→48.746 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: FREE R-VALUE / ESU R: 1.189 / ESU R Free: 0.403
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2754 1297 4.845 %
Rwork0.2313 25472 -
all0.234 --
obs-26769 99.884 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 87.384 Å2
Baniso -1Baniso -2Baniso -3
1-1.464 Å2-0 Å2-0 Å2
2--1.464 Å2-0 Å2
3----2.929 Å2
Refinement stepCycle: LAST / Resolution: 3→48.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 50 22 5852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135937
X-RAY DIFFRACTIONr_bond_other_d0.0350.0165682
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.658032
X-RAY DIFFRACTIONr_angle_other_deg2.3291.58113156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9685734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23724.618288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.871151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5381521
X-RAY DIFFRACTIONr_chiral_restr0.0670.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026655
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021239
X-RAY DIFFRACTIONr_nbd_refined0.2270.21460
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2420.25882
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22831
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2152
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4470.218
X-RAY DIFFRACTIONr_nbd_other0.1970.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3210.21
X-RAY DIFFRACTIONr_mcbond_it6.3869.1462948
X-RAY DIFFRACTIONr_mcbond_other6.3859.1442947
X-RAY DIFFRACTIONr_mcangle_it9.82913.7113678
X-RAY DIFFRACTIONr_mcangle_other9.82813.7143679
X-RAY DIFFRACTIONr_scbond_it6.359.5052988
X-RAY DIFFRACTIONr_scbond_other6.3499.5062987
X-RAY DIFFRACTIONr_scangle_it9.74314.0384354
X-RAY DIFFRACTIONr_scangle_other9.74214.0374355
X-RAY DIFFRACTIONr_lrange_it13.599108.3966587
X-RAY DIFFRACTIONr_lrange_other13.598108.3866588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3-3.0780.339890.30918470.31119360.7780.7621000.298
3.078-3.1620.326730.28918070.2918810.7660.899.94680.273
3.162-3.2530.311840.26417540.26618380.8060.8481000.243
3.253-3.3530.2991020.25216840.25517860.860.8611000.224
3.353-3.4620.279950.25416480.25617430.8640.8981000.233
3.462-3.5830.282880.22515990.22816870.8950.9121000.201
3.583-3.7170.292590.24615630.24716220.8720.8981000.221
3.717-3.8680.241890.22414780.22515670.9180.9121000.19
3.868-4.0390.256960.19514010.19915030.9310.93899.60080.161
4.039-4.2350.228790.17913720.18214520.9450.94899.93110.145
4.235-4.4620.247490.18813280.1913770.9360.9441000.147
4.462-4.730.246580.18712580.18913160.930.9441000.151
4.73-5.0530.22340.20411980.20412320.930.9351000.168
5.053-5.4530.295550.22611000.22911550.90.9161000.177
5.453-5.9660.312540.25110290.25410830.8830.8991000.204
5.966-6.6580.299530.2549190.2579720.8840.9051000.214
6.658-7.6640.25490.2288310.2298860.9130.92699.32280.197
7.664-9.3290.272470.217010.2137560.910.94398.94180.193
9.329-12.9580.305250.2225810.2266060.8990.9351000.215
12.958-48.7460.372190.4393730.4363920.8530.8061000.394

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