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- PDB-7yan: UDP-glucuronosyltransferase2B17 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7yan
TitleUDP-glucuronosyltransferase2B17 C-terminal domain
ComponentsUDP-glucuronosyltransferase 2B17
KeywordsTRANSFERASE / Complex / truncation
Function / homology
Function and homology information


glucuronosyltransferase / : / Glucuronidation / glucuronosyltransferase activity / estrogen metabolic process / Prednisone ADME / Aspirin ADME / steroid metabolic process / xenobiotic metabolic process / endoplasmic reticulum membrane / membrane
Similarity search - Function
: / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
L(+)-TARTARIC ACID / UDP-glucuronosyltransferase 2B17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, C.Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: UDP-glucuronosyltransferase2B17 C-terminal domain
Authors: Wang, C.Y. / Zhang, L.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: UDP-glucuronosyltransferase 2B17
B: UDP-glucuronosyltransferase 2B17
C: UDP-glucuronosyltransferase 2B17
D: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7858
Polymers84,1854
Non-polymers6004
Water82946
1
A: UDP-glucuronosyltransferase 2B17
B: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3934
Polymers42,0932
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-11 kcal/mol
Surface area14390 Å2
MethodPISA
2
C: UDP-glucuronosyltransferase 2B17
hetero molecules

D: UDP-glucuronosyltransferase 2B17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3934
Polymers42,0932
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2560 Å2
ΔGint-11 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.150, 57.308, 74.074
Angle α, β, γ (deg.)99.245, 94.715, 90.118
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
UDP-glucuronosyltransferase 2B17 / UDPGT 2B17 / UGT2B17 / C19-steroid-specific UDP-glucuronosyltransferase / C19-steroid-specific UDPGT


Mass: 21046.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGT2B17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75795, glucuronosyltransferase
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 6000, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→19.11 Å / Num. obs: 20837 / % possible obs: 97.45 % / Redundancy: 2.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.0978 / Net I/σ(I): 8.05
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 2019 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IPB

6ipb


Resolution: 2.5→19.11 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.763 / SU B: 17.612 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.432
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3308 1012 4.857 %
Rwork0.2677 19825 -
all0.271 --
obs-20837 97.469 %
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: 18.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20.001 Å20.025 Å2
2--0.002 Å2-0.027 Å2
3----0.006 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 40 46 5138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174907
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6447014
X-RAY DIFFRACTIONr_angle_other_deg1.1381.57611473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60724.182220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18415941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021516
X-RAY DIFFRACTIONr_chiral_restr0.0510.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.2110.21182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24689
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22432
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2132
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1430.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.241
X-RAY DIFFRACTIONr_nbd_other0.3360.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4140.21
X-RAY DIFFRACTIONr_mcbond_it1.2251.892613
X-RAY DIFFRACTIONr_mcbond_other1.2241.8892612
X-RAY DIFFRACTIONr_mcangle_it2.1532.8313260
X-RAY DIFFRACTIONr_mcangle_other2.1532.8323261
X-RAY DIFFRACTIONr_scbond_it1.1082.0032583
X-RAY DIFFRACTIONr_scbond_other1.1082.0042580
X-RAY DIFFRACTIONr_scangle_it1.9172.9413754
X-RAY DIFFRACTIONr_scangle_other1.9172.9413753
X-RAY DIFFRACTIONr_lrange_it4.68822.4325671
X-RAY DIFFRACTIONr_lrange_other4.68922.4335668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.448700.3031434X-RAY DIFFRACTION92.8395
2.565-2.6350.423740.2991399X-RAY DIFFRACTION97.2277
2.635-2.7110.424690.2991431X-RAY DIFFRACTION98.7492
2.711-2.7950.388770.291336X-RAY DIFFRACTION99.3671
2.795-2.8860.327860.3251346X-RAY DIFFRACTION99.5828
2.886-2.9870.445670.3081302X-RAY DIFFRACTION99.7087
2.987-3.10.325640.2811210X-RAY DIFFRACTION99.376
3.1-3.2260.352490.271212X-RAY DIFFRACTION99.6051
3.226-3.3690.324490.2441165X-RAY DIFFRACTION99.0212
3.369-3.5330.314400.2571107X-RAY DIFFRACTION99.3934
3.533-3.7240.347500.2581030X-RAY DIFFRACTION98.7203
3.724-3.9490.264440.245979X-RAY DIFFRACTION97.6145
3.949-4.2210.245500.227916X-RAY DIFFRACTION98.0711
4.221-4.5580.271410.235842X-RAY DIFFRACTION97.033
4.558-4.9910.326440.256766X-RAY DIFFRACTION96.5435
4.991-5.5770.293470.271696X-RAY DIFFRACTION96.8709
5.577-6.4340.352300.273616X-RAY DIFFRACTION96.4179
6.434-7.8640.277330.256497X-RAY DIFFRACTION93.8053
7.864-11.0570.216200.223379X-RAY DIFFRACTION91.3044
11.057-19.110.23380.286162X-RAY DIFFRACTION68.5484

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