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- PDB-6rjk: Structure of virulence factor SghA from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 6rjk
TitleStructure of virulence factor SghA from Agrobacterium tumefaciens
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
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 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 1.3Jan 24, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,7472
Polymers109,7472
Non-polymers00
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Two monomer forms homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-10 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.240, 80.390, 184.620
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 47.76 % / Description: plate
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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 73481 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.07 / Rrim(I) all: 0.11 / Net I/σ(I): 8.8
Reflection shellResolution: 1.92→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4498 / CC1/2: 0.71 / Rpim(I) all: 0.45 / Rrim(I) all: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NP2

1np2


Resolution: 1.922→48.428 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.21 3694 5.04 %
Rwork0.1738 --
obs0.1756 73326 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.922→48.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7139 0 0 950 8089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087359
X-RAY DIFFRACTIONf_angle_d1.08810009
X-RAY DIFFRACTIONf_dihedral_angle_d12.9192599
X-RAY DIFFRACTIONf_chiral_restr0.0751020
X-RAY DIFFRACTIONf_plane_restr0.0051313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.922-1.94730.31031320.25092672X-RAY DIFFRACTION100
1.9473-1.9740.24651410.23422641X-RAY DIFFRACTION100
1.974-2.00220.27831400.23592640X-RAY DIFFRACTION100
2.0022-2.03210.27191390.22472632X-RAY DIFFRACTION100
2.0321-2.06380.29211440.21962673X-RAY DIFFRACTION100
2.0638-2.09770.25261500.2172630X-RAY DIFFRACTION100
2.0977-2.13380.27391520.20692653X-RAY DIFFRACTION100
2.1338-2.17260.26271470.20812633X-RAY DIFFRACTION100
2.1726-2.21440.31011480.20142633X-RAY DIFFRACTION99
2.2144-2.25960.25591480.19982640X-RAY DIFFRACTION100
2.2596-2.30880.25141450.19462666X-RAY DIFFRACTION100
2.3088-2.36250.21691490.18052648X-RAY DIFFRACTION99
2.3625-2.42150.24291410.18752618X-RAY DIFFRACTION99
2.4215-2.4870.21671350.18892694X-RAY DIFFRACTION100
2.487-2.56020.19571550.17362650X-RAY DIFFRACTION100
2.5602-2.64280.21271390.1772680X-RAY DIFFRACTION100
2.6428-2.73730.19711320.17672668X-RAY DIFFRACTION100
2.7373-2.84690.21241350.17752705X-RAY DIFFRACTION100
2.8469-2.97640.26311340.17752711X-RAY DIFFRACTION100
2.9764-3.13330.19451400.18112676X-RAY DIFFRACTION100
3.1333-3.32960.20921310.17092726X-RAY DIFFRACTION100
3.3296-3.58660.18541290.15772708X-RAY DIFFRACTION100
3.5866-3.94740.15071450.14632723X-RAY DIFFRACTION100
3.9474-4.51820.1621370.12952741X-RAY DIFFRACTION99
4.5182-5.6910.17481420.132702X-RAY DIFFRACTION97
5.691-48.4430.15581640.15372869X-RAY DIFFRACTION99

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