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- PDB-3k46: Crystal structure of full-length E. coli beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 3k46
TitleCrystal structure of full-length E. coli beta-glucuronidase
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / alpha/beta barrel / sugar-binding domain / beta-sandwich domain / glycosyl hydrolase / Glycosidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWallace, B.D. / Lane, K.T. / Redinbo, M.R.
CitationJournal: Science / Year: 2010
Title: Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.
Authors: Wallace, B.D. / Wang, H. / Lane, K.T. / Scott, J.E. / Orans, J. / Koo, J.S. / Venkatesh, M. / Jobin, C. / Yeh, L.A. / Mani, S. / Redinbo, M.R.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)137,4942
Polymers137,4942
Non-polymers00
Water6,431357
1
A: Beta-glucuronidase
B: Beta-glucuronidase

A: Beta-glucuronidase
B: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)274,9884
Polymers274,9884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13240 Å2
ΔGint-93 kcal/mol
Surface area82390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.745, 76.193, 125.666
Angle α, β, γ (deg.)90.00, 125.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

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Components

#1: Protein Beta-glucuronidase / GUS / Beta-D-glucuronoside glucuronosohydrolase


Mass: 68746.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1617, gurA, gusA, JW1609, uidA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05804, beta-glucuronidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 289 K / pH: 7.4
Details: 15% PEG 3350, 0.2M Mg Acetate, 0.02% Sodium azide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. obs: 43689 / % possible obs: 96.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.452 / % possible all: 82.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.63 Å
Translation3 Å47.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K4A

3k4a


Resolution: 2.5→30.62 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.7 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 2205 5.07 %
Rwork0.214 --
obs0.217 43507 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.5 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 80.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.889 Å20 Å2-0.098 Å2
2--18.59 Å2-0 Å2
3----5.701 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 0 357 9918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039815
X-RAY DIFFRACTIONf_angle_d0.81513353
X-RAY DIFFRACTIONf_dihedral_angle_d18.0993455
X-RAY DIFFRACTIONf_chiral_restr0.0621418
X-RAY DIFFRACTIONf_plane_restr0.0041742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.497-2.55150.39451050.28631885X-RAY DIFFRACTION71
2.5515-2.61080.35231360.27772252X-RAY DIFFRACTION85
2.6108-2.67610.33721450.27452433X-RAY DIFFRACTION90
2.6761-2.74840.33241400.26772479X-RAY DIFFRACTION94
2.7484-2.82920.33541390.24212650X-RAY DIFFRACTION98
2.8292-2.92040.33611460.25512643X-RAY DIFFRACTION99
2.9204-3.02470.29871230.24862668X-RAY DIFFRACTION99
3.0247-3.14570.31521480.24152665X-RAY DIFFRACTION99
3.1457-3.28870.291410.22372676X-RAY DIFFRACTION99
3.2887-3.46190.25151210.21022693X-RAY DIFFRACTION99
3.4619-3.67850.25381400.20782674X-RAY DIFFRACTION99
3.6785-3.96190.27671620.18182645X-RAY DIFFRACTION99
3.9619-4.35960.21381280.17112708X-RAY DIFFRACTION100
4.3596-4.98810.1741470.15722705X-RAY DIFFRACTION100
4.9881-6.27560.23311400.18972733X-RAY DIFFRACTION100
6.2756-30.62330.24161440.19512793X-RAY DIFFRACTION99

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