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- PDB-6ncy: Crystal structure of hybrid beta-glucuronidase/beta-galacturonida... -

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Basic information

Entry
Database: PDB / ID: 6ncy
TitleCrystal structure of hybrid beta-glucuronidase/beta-galacturonidase from Fusicatenibacter saccharivorans
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / glycoside hydrolase family 2 / beta-glucuronidase / beta-galacturonidase
Function / homology
Function and homology information


beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / beta-galactosidase
Similarity search - Component
Biological speciesFusicatenibacter saccharivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsWalton, W.G. / Pellock, S.J. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biochemistry / Year: 2019
Title: Selecting a Single Stereocenter: The Molecular Nuances That Differentiate beta-Hexuronidases in the Human Gut Microbiome.
Authors: Pellock, S.J. / Walton, W.G. / Redinbo, M.R.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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)143,38512
Polymers142,5282
Non-polymers85710
Water20,5011138
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)430,15536
Polymers427,5836
Non-polymers2,57130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27030 Å2
ΔGint-138 kcal/mol
Surface area120450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.562, 192.562, 192.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Beta-glucuronidase /


Mass: 71263.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusicatenibacter saccharivorans (bacteria)
Gene: uidA_2, ERS852406_01826 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174EHD1, beta-glucuronidase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1138 / 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: 4.17 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M DL-malic acid, pH 7.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.05→29.713 Å / Num. obs: 147997 / % possible obs: 99.9 % / Redundancy: 34.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.028 / Net I/σ(I): 21.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.711 / Num. unique obs: 14676 / CC1/2: 0.578 / Rpim(I) all: 0.46 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.05→29.713 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4
RfactorNum. reflection% reflection
Rfree0.18 1988 1.34 %
Rwork0.1539 --
obs0.1543 147980 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→29.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9580 0 49 1138 10767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089916
X-RAY DIFFRACTIONf_angle_d0.89913415
X-RAY DIFFRACTIONf_dihedral_angle_d17.8145954
X-RAY DIFFRACTIONf_chiral_restr0.0611416
X-RAY DIFFRACTIONf_plane_restr0.0061735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0502-2.10140.26431440.255810317X-RAY DIFFRACTION100
2.1014-2.15820.23731390.2210357X-RAY DIFFRACTION100
2.1582-2.22170.22431390.194310370X-RAY DIFFRACTION100
2.2217-2.29340.20521400.179310364X-RAY DIFFRACTION100
2.2934-2.37530.18931440.162810340X-RAY DIFFRACTION100
2.3753-2.47040.19511420.156810390X-RAY DIFFRACTION100
2.4704-2.58280.19251420.155810389X-RAY DIFFRACTION100
2.5828-2.71880.18471380.151710428X-RAY DIFFRACTION100
2.7188-2.8890.18011440.159810395X-RAY DIFFRACTION100
2.889-3.11190.19211410.158310406X-RAY DIFFRACTION100
3.1119-3.42460.17761450.151710451X-RAY DIFFRACTION100
3.4246-3.91920.18251380.134110470X-RAY DIFFRACTION100
3.9192-4.93420.1511430.122410568X-RAY DIFFRACTION100
4.9342-29.71610.15051490.158810747X-RAY DIFFRACTION100

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