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- PDB-6rjm: Complex structure of virulence factor SghA and its hydrolysis pro... -

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Basic information

Entry
Database: PDB / ID: 6rjm
TitleComplex structure of virulence factor SghA and its hydrolysis product glucose
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Chemical signaling / Sucrose / Agrobacterium / Host-pathogen interaction / Glucosidase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 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 27, 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 ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
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)110,1074
Polymers109,7472
Non-polymers3602
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-6 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.035, 84.590, 184.732
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: 54873.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens A6 (bacteria)
Gene: sghA / Plasmid: pET14b-SghA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I4PGZ0, beta-glucosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
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: PSI PILATUS 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: 2.1→50 Å / Num. obs: 98373 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.24 Å / Redundancy: 3.3 % / Num. unique obs: 4123 / CC1/2: 0.7 / Rpim(I) all: 0.369 / Rrim(I) all: 0.692 / Rsym value: 0.572 / % possible all: 97.3

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Processing

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

6rjk


Resolution: 2.112→49.784 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.23 4966 5.05 %
Rwork0.1814 --
obs0.1838 98364 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.112→49.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 0 24 441 7647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087428
X-RAY DIFFRACTIONf_angle_d1.08610103
X-RAY DIFFRACTIONf_dihedral_angle_d13.52629
X-RAY DIFFRACTIONf_chiral_restr0.0741035
X-RAY DIFFRACTIONf_plane_restr0.0051322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1121-2.13610.34751500.31232632X-RAY DIFFRACTION83
2.1361-2.16120.36511660.29313180X-RAY DIFFRACTION98
2.1612-2.18760.32981860.26873187X-RAY DIFFRACTION98
2.1876-2.21530.31981590.27183120X-RAY DIFFRACTION98
2.2153-2.24440.36131970.27263139X-RAY DIFFRACTION98
2.2444-2.27520.3091680.26083202X-RAY DIFFRACTION97
2.2752-2.30770.30691540.25063117X-RAY DIFFRACTION96
2.3077-2.34210.30361910.23883124X-RAY DIFFRACTION97
2.3421-2.37870.25841640.22813138X-RAY DIFFRACTION97
2.3787-2.41770.24491780.22283100X-RAY DIFFRACTION97
2.4177-2.45940.28631740.21733140X-RAY DIFFRACTION95
2.4594-2.50410.23861430.22223051X-RAY DIFFRACTION95
2.5041-2.55230.25161810.19713088X-RAY DIFFRACTION94
2.5523-2.60440.23821690.19392985X-RAY DIFFRACTION94
2.6044-2.6610.27661780.19643200X-RAY DIFFRACTION98
2.661-2.72290.25221950.20043161X-RAY DIFFRACTION98
2.7229-2.7910.25811460.19433206X-RAY DIFFRACTION98
2.791-2.86640.25651460.19573150X-RAY DIFFRACTION97
2.8664-2.95080.28621470.20053184X-RAY DIFFRACTION97
2.9508-3.0460.28051590.20023082X-RAY DIFFRACTION96
3.046-3.15480.2571480.20383097X-RAY DIFFRACTION95
3.1548-3.28110.25171480.19323080X-RAY DIFFRACTION94
3.2811-3.43040.21691510.1793033X-RAY DIFFRACTION94
3.4304-3.61120.20081570.16023176X-RAY DIFFRACTION98
3.6112-3.83740.17831930.15683209X-RAY DIFFRACTION98
3.8374-4.13360.20561620.14423166X-RAY DIFFRACTION98
4.1336-4.54930.17361540.13013120X-RAY DIFFRACTION96
4.5493-5.2070.19081680.13223009X-RAY DIFFRACTION93
5.207-6.55790.18021420.153251X-RAY DIFFRACTION99
6.5579-49.79760.17131920.14583071X-RAY DIFFRACTION96

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