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- PDB-7cdx: Complex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR wit... -

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Basic information

Entry
Database: PDB / ID: 7cdx
TitleComplex STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR with its effector sucrose
ComponentsLacI-type transcription factor
KeywordsTRANSCRIPTION / AGROBACTERIUM INFECTION / PLANT-MICROBE INTERACTION / LACI REP SUCROSE
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / LacI-type transcription factor
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsYe, F.Z. / Wang, C. / Yan, X.F. / Zhang, L.H. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-RF2009-RF001-267 Singapore
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of a novel repressor, SghR, controllingAgrobacteriuminfection by cross-talking to plants.
Authors: Ye, F. / Wang, C. / Fu, Q. / Yan, X.F. / Bharath, S.R. / Casanas, A. / Wang, M. / Song, H. / Zhang, L.H. / Gao, Y.G.
History
DepositionJun 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 9, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LacI-type transcription factor
B: LacI-type transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2374
Polymers81,5532
Non-polymers6852
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-18 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.678, 120.146, 122.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LacI-type transcription factor


Mass: 40776.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens A6 (bacteria)
Gene: sghR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2I4PGE9
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.61 Å3/Da / Density % sol: 23.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05M HEPES-Na pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9985 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9985 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 58464 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rpim(I) all: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 31106 / Rsym value: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDV

7cdv


Resolution: 2.103→42.832 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 34.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 2940 5.03 %
Rwork0.2252 55524 -
obs0.2275 58464 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.24 Å2 / Biso mean: 21.18 Å2 / Biso min: 3.7 Å2
Refinement stepCycle: final / Resolution: 2.103→42.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 46 196 4487
Biso mean--27.34 21.51 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014382
X-RAY DIFFRACTIONf_angle_d1.2685943
X-RAY DIFFRACTIONf_chiral_restr0.083681
X-RAY DIFFRACTIONf_plane_restr0.005765
X-RAY DIFFRACTIONf_dihedral_angle_d15.2061637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1035-2.13790.39311320.3735241092
2.1379-2.17480.45131410.3297263399
2.1748-2.21440.34171470.3166270999
2.2144-2.25690.29611380.3087259599
2.2569-2.3030.28041370.28882662100
2.303-2.35310.331410.27852694100
2.3531-2.40780.37321380.26332668100
2.4078-2.4680.3571350.26542609100
2.468-2.53470.35241460.25532721100
2.5347-2.60930.30991430.25332625100
2.6093-2.69350.31271400.25082667100
2.6935-2.78980.26621340.23382639100
2.7898-2.90150.27171420.22672667100
2.9015-3.03350.28321440.24112645100
3.0335-3.19340.29661370.21822678100
3.1934-3.39340.28421410.2262630100
3.3934-3.65520.23631380.21692690100
3.6552-4.02280.25311410.2021264099
4.0228-4.60430.22481410.17462652100
4.6043-5.79870.19921420.1838265699
5.7987-42.820.20551420.1806263499

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