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- PDB-7cdv: STRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR -

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Basic information

Entry
Database: PDB / ID: 7cdv
TitleSTRUCTURE OF A NOVEL VIRULENCE REGULATION FACTOR SghR
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
LacI-type transcription factor
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 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


Theoretical massNumber of molelcules
Total (without water)81,5532
Polymers81,5532
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-28 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.530, 119.440, 121.920
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 / Plasmid: PET14B-SGHR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODONPLUS-(DE3) RIL / References: UniProt: A0A2I4PGE9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.59 Å3/Da / Density % sol: 22.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M HEPES-NA PH 7.0, 20% PEG 3350, 1%(W/V) TRYPTONE, VAPOR DIFFUSION, TEMPERATURE 293K

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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 PILATUS 6M-F / Detector: PIXEL / Date: Dec 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31202 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rsym value: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 31202 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIXDEV_1932refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GV0

3gv0


Resolution: 2.1→42.66 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1654 5.32 %
Rwork0.202 29423 -
obs0.204 31077 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.6 Å2 / Biso mean: 26.854 Å2 / Biso min: 6.45 Å2
Refinement stepCycle: final / Resolution: 2.1→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 0 385 4682
Biso mean---32.23 -
Num. residues----553
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16180.30171070.2572404100
2.1618-2.23160.29551420.2382242399
2.2316-2.31130.26721240.23382412100
2.3113-2.40390.27631560.22862416100
2.4039-2.51330.26951360.22432430100
2.5133-2.64570.28351650.22532405100
2.6457-2.81150.28441520.22082422100
2.8115-3.02850.25621290.21772459100
3.0285-3.33320.21151460.19942453100
3.3332-3.81520.20421440.17562484100
3.8152-4.80570.19041200.1603252199
4.8057-42.660.22011330.1886259497
Refinement TLS params.Method: refined / Origin x: 0.0415 Å / Origin y: 1.6577 Å / Origin z: 26.9851 Å
111213212223313233
T0.0429 Å2-0.0142 Å20.0023 Å2-0.082 Å20.0049 Å2--0.0752 Å2
L0.0604 °2-0.0067 °20.0735 °2-0.416 °20.2102 °2--0.4036 °2
S-0.0388 Å °0.0312 Å °0.003 Å °-0.0302 Å °0.0168 Å °-0.0102 Å °-0.0212 Å °0.0372 Å °-0.0068 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA73 - 349
2X-RAY DIFFRACTION1ALLA401 - 592
3X-RAY DIFFRACTION1ALLB74 - 349
4X-RAY DIFFRACTION1ALLB401 - 593

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