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- PDB-4jkl: Crystal Structure of Streptococcus agalactiae beta-glucuronidase ... -

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Basic information

Entry
Database: PDB / ID: 4jkl
TitleCrystal Structure of Streptococcus agalactiae beta-glucuronidase in space group P21212
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / alpha/beta barrel / beta-sandwich / sugar-binding domain / glycosyl hydrolase
Function / homology
Function and homology information


beta-glucuronidase / beta-galactosidase activity / carbohydrate metabolic process
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 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.288 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6096
Polymers139,5122
Non-polymers974
Water13,944774
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,21812
Polymers279,0244
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area16980 Å2
ΔGint-97 kcal/mol
Surface area76150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.001, 198.759, 75.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-997-

HOH

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Components

#1: Protein Beta-glucuronidase /


Mass: 69755.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG0698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI (DE3) / References: UniProt: Q8E0N2, beta-glucuronidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20-28% PEG 3350, 0.1-0.3 M KSCN, 0.02% sodium azide, vapor diffusion, hanging drop, temperature 289.15K

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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: Nov 29, 2011
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: 2.288→100 Å / Num. obs: 57552 / % possible obs: 98.3 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.158 / Χ2: 0.857 / Net I/σ(I): 4.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.387.20.47652490.681190.9
2.38-2.488.20.43354150.677194.6
2.48-2.599.40.41356970.703198
2.59-2.7311.20.39457570.715199.7
2.73-2.913.30.34157880.7641100
2.9-3.1214.60.26958160.8011100
3.12-3.44150.16858520.8211100
3.44-3.9314.90.11958710.9941100
3.93-4.9614.80.09159261.1111100
4.96-10014.20.07661810.985199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.288→37.306 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8437 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2819 4.91 %random
Rwork0.1744 ---
obs0.1769 57471 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.89 Å2 / Biso mean: 19.9065 Å2 / Biso min: 1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.288→37.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9575 0 4 774 10353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029878
X-RAY DIFFRACTIONf_angle_d0.72913408
X-RAY DIFFRACTIONf_chiral_restr0.0531448
X-RAY DIFFRACTIONf_plane_restr0.0031750
X-RAY DIFFRACTIONf_dihedral_angle_d13.9343684
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2882-2.32770.31711270.24362301242885
2.3277-2.370.28051410.2142542268392
2.37-2.41560.28411130.20752567268093
2.4156-2.46490.26191370.2122612274996
2.4649-2.51850.27431440.21072708285298
2.5185-2.5770.2831230.20792712283598
2.577-2.64150.27061520.204627192871100
2.6415-2.71290.27051520.202327492901100
2.7129-2.79270.28291480.193927522900100
2.7927-2.88280.26351560.191427342890100
2.8828-2.98580.23231490.193627722921100
2.9858-3.10530.25861530.189227602913100
3.1053-3.24650.2571320.187827832915100
3.2465-3.41760.21441380.166128042942100
3.4176-3.63150.20841620.158327692931100
3.6315-3.91160.21321220.157528252947100
3.9116-4.30480.16441200.139228352955100
4.3048-4.92650.14751390.127228422981100
4.9265-6.20220.20351540.151128643018100
6.2022-37.31140.1791570.172730023159100

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