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- PDB-6rjo: Complex structure of virulence factor SghA with its substrate ana... -

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Basic information

Entry
Database: PDB / ID: 6rjo
TitleComplex structure of virulence factor SghA with its substrate analog salicin
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Chemical signaling / Sucrose / Agrobacterium / Host-pathogen interaction / Glucosidase
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-(hydroxymethyl)phenyl beta-D-glucopyranoside / Beta-glucosidase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsYe, F.Z. / Wang, C. / Chang, C.Q. / Zhang, L.H. / Gao, Y.G.
Funding support Singapore, China, 2items
OrganizationGrant numberCountry
National Research Foundation (Singapore)NRF-RF2009-RF001-267 Singapore
National Basic Research Program of China (973 Program)2015CB150600 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Agrobacteria reprogram virulence gene expression by controlled release of host-conjugated signals.
Authors: Wang, C. / Ye, F. / Chang, C. / Liu, X. / Wang, J. / Wang, J. / Yan, X.F. / Fu, Q. / Zhou, J. / Chen, S. / Gao, Y.G. / Zhang, L.H.
History
DepositionApr 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 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_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: chem_comp / pdbx_audit_support ...chem_comp / pdbx_audit_support / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_audit_support.funding_organization
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2364
Polymers109,6632
Non-polymers5732
Water16,466914
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-11 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.747, 81.008, 183.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucosidase


Mass: 54831.547 Da / Num. of mol.: 2 / Mutation: E179S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens A6 (bacteria)
Gene: sghA / Plasmid: pET14b-SghA-E179S / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I4PGZ0, beta-glucosidase
#2: Sugar ChemComp-SA0 / 2-(hydroxymethyl)phenyl beta-D-glucopyranoside / Salicin / 2-(hydroxymethyl)phenyl beta-D-glucoside / 2-(hydroxymethyl)phenyl D-glucoside / 2-(hydroxymethyl)phenyl glucoside


Type: D-saccharide / Mass: 286.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C13H18O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 914 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 and 0.4 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 86072 / % possible obs: 97.3 % / Redundancy: 3 % / Biso Wilson estimate: 12.1 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Rsym value: 0.07 / Net I/σ(I): 12.1
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.9 % / Num. unique obs: 4431 / Rpim(I) all: 0.5 / Rrim(I) all: 0.9 / Rsym value: 0.6 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SJK

6sjk


Resolution: 1.804→48.856 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.2095 7649 5.03 %
Rwork0.1731 --
obs0.1749 152164 89.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→48.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7133 0 40 914 8087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077395
X-RAY DIFFRACTIONf_angle_d1.08410059
X-RAY DIFFRACTIONf_dihedral_angle_d15.8992651
X-RAY DIFFRACTIONf_chiral_restr0.0741020
X-RAY DIFFRACTIONf_plane_restr0.0051313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8039-1.82440.34452400.29664539X-RAY DIFFRACTION85
1.8244-1.84590.35442590.28544828X-RAY DIFFRACTION89
1.8459-1.86840.29232480.27374683X-RAY DIFFRACTION88
1.8684-1.89210.29812530.26614706X-RAY DIFFRACTION87
1.8921-1.9170.2632470.26084633X-RAY DIFFRACTION87
1.917-1.94320.27872480.25524726X-RAY DIFFRACTION88
1.9432-1.9710.25752530.23774773X-RAY DIFFRACTION90
1.971-2.00040.2752640.24244848X-RAY DIFFRACTION90
2.0004-2.03170.32842550.24094839X-RAY DIFFRACTION90
2.0317-2.0650.2592550.2274880X-RAY DIFFRACTION91
2.065-2.10060.28222530.21634763X-RAY DIFFRACTION90
2.1006-2.13880.24532570.20064873X-RAY DIFFRACTION90
2.1388-2.17990.24952490.19864834X-RAY DIFFRACTION90
2.1799-2.22440.25832480.20024817X-RAY DIFFRACTION90
2.2244-2.27280.24932510.19394770X-RAY DIFFRACTION89
2.2728-2.32570.2532530.18374758X-RAY DIFFRACTION88
2.3257-2.38380.21962650.17984884X-RAY DIFFRACTION91
2.3838-2.44830.22022550.17314974X-RAY DIFFRACTION92
2.4483-2.52030.23012600.16974866X-RAY DIFFRACTION92
2.5203-2.60160.21142520.16754927X-RAY DIFFRACTION92
2.6016-2.69460.21652550.16744946X-RAY DIFFRACTION92
2.6946-2.80250.21672620.1674918X-RAY DIFFRACTION92
2.8025-2.930.2242670.16874844X-RAY DIFFRACTION90
2.93-3.08450.18522510.16874852X-RAY DIFFRACTION90
3.0845-3.27770.20542680.16314898X-RAY DIFFRACTION92
3.2777-3.53070.19752640.15524919X-RAY DIFFRACTION91
3.5307-3.88590.15692470.13954840X-RAY DIFFRACTION91
3.8859-4.44790.16042480.12244742X-RAY DIFFRACTION88
4.4479-5.60250.14172630.12714848X-RAY DIFFRACTION91
5.6025-48.87440.14322590.13924787X-RAY DIFFRACTION89

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