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- PDB-2o6l: Crystal Structure of the UDP-Glucuronic Acid Binding Domain of th... -

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Basic information

Entry
Database: PDB / ID: 2o6l
TitleCrystal Structure of the UDP-Glucuronic Acid Binding Domain of the Human Drug Metabolizing UDP-Glucuronosyltransferase 2B7
ComponentsUDP-glucuronosyltransferase 2B7
KeywordsTRANSFERASE / Drug metabolism / rossman / MAD / enzyme / nucleotide binding / sugar / UDP-glucuronosyltransferase / UGT
Function / homology
Function and homology information


glucuronosyltransferase / cellular glucuronidation / Glucuronidation / glucuronosyltransferase activity / estrogen metabolic process / Prednisone ADME / Aspirin ADME / androgen metabolic process / xenobiotic metabolic process / lipid metabolic process ...glucuronosyltransferase / cellular glucuronidation / Glucuronidation / glucuronosyltransferase activity / estrogen metabolic process / Prednisone ADME / Aspirin ADME / androgen metabolic process / xenobiotic metabolic process / lipid 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 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-glucuronosyltransferase 2B7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMiley, M.J. / Redinbo, M.R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Cofactor-Binding Domain of the Human Phase II Drug-Metabolism Enzyme UDP-Glucuronosyltransferase 2B7.
Authors: Miley, M.J. / Zielinska, A.K. / Keenan, J.E. / Bratton, S.M. / Radominska-Pandya, A. / Redinbo, M.R.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucuronosyltransferase 2B7
B: UDP-glucuronosyltransferase 2B7


Theoretical massNumber of molelcules
Total (without water)38,2512
Polymers38,2512
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.175, 75.175, 218.296
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-582-

HOH

31A-586-

HOH

41A-587-

HOH

51A-588-

HOH

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Components

#1: Protein UDP-glucuronosyltransferase 2B7 / UDPGT / 3 / 4- catechol estrogen specific / UDPGTh-2


Mass: 19125.721 Da / Num. of mol.: 2
Fragment: UDP-Glucuronic acid binding domain, residues 285-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGT2B7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P16662, glucuronosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12-16% PEG 4000, 100 mM K2CO3, 100 mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97925, 0.97942, 0.97174, 0.98089
APS 22-ID2
APS 22-ID3
APS 22-ID4
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979421
30.971741
40.980891
ReflectionResolution: 1.8→50 Å / Num. all: 34624 / Num. obs: 33813 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 5.6 / Net I/σ(I): 50
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 3171 / Rsym value: 39.2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→48.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 103739.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
Details: MAD 3 wavelengths were used to solve structure to 2.1 angstroms (multi-wavelength method, wavelengths 0.97925, 0.97942, 0.97174). Once model traced and refined, 1.80 angstrom dataset was ...Details: MAD 3 wavelengths were used to solve structure to 2.1 angstroms (multi-wavelength method, wavelengths 0.97925, 0.97942, 0.97174). Once model traced and refined, 1.80 angstrom dataset was used for final refinements (low-remote-dataset, wavelength 0.98089).
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2991 4.9 %RANDOM
Rwork0.219 ---
obs0.219 33813 95.4 %-
all-33813 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1013 Å2 / ksol: 0.325832 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å21.82 Å20 Å2
2--2.76 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 283 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 460 5.1 %
Rwork0.296 8513 -
obs-8513 84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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