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- PDB-4jkm: Crystal Structure of Clostridium perfringens beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 4jkm
TitleCrystal Structure of Clostridium perfringens beta-glucuronidase
Components
  • Beta-glucuronidase
  • Maltose-binding periplasmic protein
KeywordsHYDROLASE / alpha/beta barrel / beta-sandwich / sugar-binding domain / glycosyl hydrolase
Function / homology
Function and homology information


beta-glucuronidase / beta-galactosidase activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...beta-glucuronidase / beta-galactosidase activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / carbohydrate metabolic process / DNA damage response / membrane
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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Galactose-binding domain-like / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Galactose-binding-like domain superfamily / D-Maltodextrin-Binding Protein; domain 2 / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Beta-glucuronidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.263 Å
AuthorsWallace, B.D. / Redinbo, M.R.
CitationJournal: Chem.Biol. / Year: 2015
Title: Structure and Inhibition of Microbiome beta-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity.
Authors: Wallace, B.D. / Roberts, A.B. / Pollet, R.M. / Ingle, J.D. / Biernat, K.A. / Pellock, S.J. / Venkatesh, M.K. / Guthrie, L. / O'Neal, S.K. / Robinson, S.J. / Dollinger, M. / Figueroa, E. / ...Authors: Wallace, B.D. / Roberts, A.B. / Pollet, R.M. / Ingle, J.D. / Biernat, K.A. / Pellock, S.J. / Venkatesh, M.K. / Guthrie, L. / O'Neal, S.K. / Robinson, S.J. / Dollinger, M. / Figueroa, E. / McShane, S.R. / Cohen, R.D. / Jin, J. / Frye, S.V. / Zamboni, W.C. / Pepe-Ranney, C. / Mani, S. / Kelly, L. / Redinbo, M.R.
History
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
D: Maltose-binding periplasmic protein
C: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)226,7104
Polymers226,7104
Non-polymers00
Water9,224512
1
A: Beta-glucuronidase
B: Beta-glucuronidase

A: Beta-glucuronidase
B: Beta-glucuronidase
D: Maltose-binding periplasmic protein
C: Maltose-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)364,8846
Polymers364,8846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_654-x+1,y,-z-1/21
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-109 kcal/mol
Surface area81740 Å2
Unit cell
Length a, b, c (Å)71.511, 292.612, 239.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

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Components

#1: Protein Beta-glucuronidase /


Mass: 69087.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: 13 / Type A / Gene: bglR / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3) / References: UniProt: Q8XP19, beta-glucuronidase
#2: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 44267.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, JW3994, malE / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3) / References: UniProt: P0AEX9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT AT POSITION 25 IS POSSIBLY DUE TO MUTATION IN THE PLASMID SEQUENCE VERSUS THE UNIPROT ENTRY.

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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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0-6.5, 28-36% PEG 400, 0.02% sodium azide, vapor diffusion, hanging drop, temperature 289.15K
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2012
RadiationMonochromator: Double crystal with K-B biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→48.77 Å / Num. obs: 117154 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.263→47.791 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.3 / σ(F): 1.33 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 5860 5.01 %
Rwork0.2066 --
obs0.2081 117081 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.6465 Å2
Baniso -1Baniso -2Baniso -3
1-3.299 Å2-0 Å20 Å2
2---2.6826 Å20 Å2
3---1.2175 Å2
Refinement stepCycle: LAST / Resolution: 2.263→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14194 0 0 512 14706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314534
X-RAY DIFFRACTIONf_angle_d0.83219753
X-RAY DIFFRACTIONf_dihedral_angle_d14.2045275
X-RAY DIFFRACTIONf_chiral_restr0.0582168
X-RAY DIFFRACTIONf_plane_restr0.0042583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2629-2.28860.35771620.32493262X-RAY DIFFRACTION88
2.2886-2.31550.32111790.28043703X-RAY DIFFRACTION100
2.3155-2.34380.2912090.27233632X-RAY DIFFRACTION100
2.3438-2.37350.33072140.26443678X-RAY DIFFRACTION100
2.3735-2.40470.28921770.25333718X-RAY DIFFRACTION100
2.4047-2.43760.32681700.25673689X-RAY DIFFRACTION100
2.4376-2.47240.29371940.2533717X-RAY DIFFRACTION100
2.4724-2.50940.30872020.25213670X-RAY DIFFRACTION100
2.5094-2.54860.29381900.2573714X-RAY DIFFRACTION100
2.5486-2.59030.29241790.243684X-RAY DIFFRACTION100
2.5903-2.6350.27862140.23323681X-RAY DIFFRACTION100
2.635-2.68290.28491700.22523698X-RAY DIFFRACTION100
2.6829-2.73450.2581940.23543722X-RAY DIFFRACTION100
2.7345-2.79030.2612060.2343688X-RAY DIFFRACTION100
2.7903-2.8510.28842030.22863688X-RAY DIFFRACTION100
2.851-2.91730.26882040.2253686X-RAY DIFFRACTION100
2.9173-2.99020.26491780.22423726X-RAY DIFFRACTION100
2.9902-3.07110.24361910.22383702X-RAY DIFFRACTION100
3.0711-3.16140.26111830.22173714X-RAY DIFFRACTION100
3.1614-3.26350.24752140.2133715X-RAY DIFFRACTION100
3.2635-3.38010.2391950.21573713X-RAY DIFFRACTION100
3.3801-3.51540.24092130.21153692X-RAY DIFFRACTION100
3.5154-3.67530.24442010.20663733X-RAY DIFFRACTION100
3.6753-3.8690.21951790.19313750X-RAY DIFFRACTION100
3.869-4.11130.2062090.17863740X-RAY DIFFRACTION100
4.1113-4.42850.17992030.17453766X-RAY DIFFRACTION100
4.4285-4.87370.1992050.16043751X-RAY DIFFRACTION100
4.8737-5.57810.21122200.16973779X-RAY DIFFRACTION100
5.5781-7.02420.21941830.20293836X-RAY DIFFRACTION100
7.0242-47.80190.1912190.20213974X-RAY DIFFRACTION100

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