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- PDB-6rk2: Complex structure of virulence factor SghA mutant with its substr... -

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Basic information

Entry
Database: PDB / ID: 6rk2
TitleComplex structure of virulence factor SghA mutant with its substrate SAG
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-(alpha-L-altropyranosyloxy)benzoic acid / Beta-glucosidase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 30, 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)110,2644
Polymers109,6632
Non-polymers6012
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.615, 80.371, 183.592
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I4PGZ0, beta-glucosidase
#2: Sugar ChemComp-6GR / 2-(alpha-L-altropyranosyloxy)benzoic acid / 2-(alpha-L-altrosyloxy)benzoic acid / 2-(L-altrosyloxy)benzoic acid / 2-(altrosyloxy)benzoic acid


Type: L-saccharide / Mass: 300.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
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: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 185327 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.9 Å2 / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Rsym value: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4523 / Rpim(I) all: 0.12 / Rrim(I) all: 0.24 / Rsym value: 0.21 / % possible all: 98.1

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Processing

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

6rjk


Resolution: 2.09→48.689 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.22
RfactorNum. reflection% reflection
Rfree0.2142 5240 5.01 %
Rwork0.1741 --
obs0.176 104529 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→48.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 42 497 7687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087412
X-RAY DIFFRACTIONf_angle_d1.1210083
X-RAY DIFFRACTIONf_dihedral_angle_d18.4862661
X-RAY DIFFRACTIONf_chiral_restr0.0751023
X-RAY DIFFRACTIONf_plane_restr0.0061317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.11380.33621740.27573347X-RAY DIFFRACTION98
2.1138-2.13860.31421740.25713313X-RAY DIFFRACTION98
2.1386-2.16470.28981710.24353327X-RAY DIFFRACTION98
2.1647-2.19210.30291770.24393370X-RAY DIFFRACTION98
2.1921-2.2210.26721780.23873290X-RAY DIFFRACTION97
2.221-2.25140.29261790.23033369X-RAY DIFFRACTION98
2.2514-2.28350.2371770.22423306X-RAY DIFFRACTION97
2.2835-2.31760.2661730.21533288X-RAY DIFFRACTION97
2.3176-2.35380.24091810.20273334X-RAY DIFFRACTION97
2.3538-2.39240.25851760.20333278X-RAY DIFFRACTION97
2.3924-2.43370.25251660.1973287X-RAY DIFFRACTION95
2.4337-2.47790.20511610.19643143X-RAY DIFFRACTION93
2.4779-2.52560.26741730.19193315X-RAY DIFFRACTION96
2.5256-2.57720.24351770.18943291X-RAY DIFFRACTION97
2.5772-2.63320.2481740.18453364X-RAY DIFFRACTION98
2.6332-2.69440.20631740.18773386X-RAY DIFFRACTION98
2.6944-2.76180.2681780.19293348X-RAY DIFFRACTION98
2.7618-2.83650.23981720.17963320X-RAY DIFFRACTION98
2.8365-2.91990.22011780.1873311X-RAY DIFFRACTION98
2.9199-3.01420.21541770.17753329X-RAY DIFFRACTION97
3.0142-3.12190.23661760.18483253X-RAY DIFFRACTION96
3.1219-3.24680.22621700.17983190X-RAY DIFFRACTION94
3.2468-3.39460.2071780.1693327X-RAY DIFFRACTION97
3.3946-3.57350.1961770.15553344X-RAY DIFFRACTION98
3.5735-3.79730.20811730.14573334X-RAY DIFFRACTION98
3.7973-4.09040.17241730.13383348X-RAY DIFFRACTION98
4.0904-4.50170.16921700.12653267X-RAY DIFFRACTION96
4.5017-5.15250.13791770.133223X-RAY DIFFRACTION95
5.1525-6.48920.1821780.14533369X-RAY DIFFRACTION99
6.4892-48.70250.1551780.14913318X-RAY DIFFRACTION97

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