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- PDB-7ce1: Complex STRUCTURE OF TRANSCRIPTION FACTOR SghR with its COGNATE DNA -

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Basic information

Entry
Database: PDB / ID: 7ce1
TitleComplex STRUCTURE OF TRANSCRIPTION FACTOR SghR with its COGNATE DNA
Components
  • LacI-type transcription factor
  • promoter DNA
KeywordsTRANSCRIPTION / AGROBACTERIUM INFECTION / PLANT-MICROBE INTERACTION / LACI REP SUCROSE
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
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 / Periplasmic binding protein-like I
Similarity search - Domain/homology
DNA / DNA (> 10) / LacI-type transcription factor
Similarity search - Component
Biological speciesAgrobacterium tumefaciens A6 (bacteria)
Agrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 21, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LacI-type transcription factor
B: LacI-type transcription factor
a: promoter DNA
b: promoter DNA
C: LacI-type transcription factor
D: LacI-type transcription factor
c: promoter DNA
d: promoter DNA
G: LacI-type transcription factor
H: LacI-type transcription factor
g: promoter DNA
h: promoter DNA
K: LacI-type transcription factor
L: LacI-type transcription factor
k: promoter DNA
l: promoter DNA
O: LacI-type transcription factor
P: LacI-type transcription factor
o: promoter DNA
p: promoter DNA
S: LacI-type transcription factor
T: LacI-type transcription factor
s: promoter DNA
t: promoter DNA


Theoretical massNumber of molelcules
Total (without water)521,79624
Polymers521,79624
Non-polymers00
Water45025
1
A: LacI-type transcription factor
B: LacI-type transcription factor
a: promoter DNA
b: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-62 kcal/mol
Surface area31960 Å2
MethodPISA
2
C: LacI-type transcription factor
D: LacI-type transcription factor
c: promoter DNA
d: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-67 kcal/mol
Surface area31650 Å2
MethodPISA
3
G: LacI-type transcription factor
H: LacI-type transcription factor
g: promoter DNA
h: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-62 kcal/mol
Surface area31230 Å2
MethodPISA
4
K: LacI-type transcription factor
L: LacI-type transcription factor
k: promoter DNA
l: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-62 kcal/mol
Surface area31440 Å2
MethodPISA
5
O: LacI-type transcription factor
P: LacI-type transcription factor
o: promoter DNA
p: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-57 kcal/mol
Surface area32570 Å2
MethodPISA
6
S: LacI-type transcription factor
T: LacI-type transcription factor
s: promoter DNA
t: promoter DNA


Theoretical massNumber of molelcules
Total (without water)86,9664
Polymers86,9664
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-48 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.900, 218.960, 284.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain G
61chain H
71chain K
81chain L
91chain O
101chain P
111chain S
121chain T
12chain a
22chain b
32chain c
42chain d
52chain g
62chain h
72chain k
82chain l
92chain o
102chain p
112chain s
122chain t

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROchain AAA18 - 3481 - 331
21GLUGLUSERSERchain BBB18 - 3451 - 328
31GLUGLULYSLYSchain CCE18 - 3491 - 332
41GLUGLUSERSERchain DDF18 - 3441 - 327
51GLUGLUPROPROchain GGI18 - 3481 - 331
61GLUGLUPROPROchain HHJ18 - 3481 - 331
71GLUGLUPROPROchain KKM18 - 3501 - 333
81GLUGLUMETMETchain LLN18 - 3461 - 329
91GLUGLUSERSERchain OOQ18 - 3451 - 328
101GLUGLUSERSERchain PPR18 - 3451 - 328
111GLUGLUSERSERchain SSU18 - 3371 - 320
121GLUGLUVALVALchain TTV18 - 3381 - 321
12DTDTDADAchain aaC1 - 181 - 18
22DTDTDADAchain bbD1 - 181 - 18
32DTDTDADAchain ccG1 - 181 - 18
42DTDTDADAchain ddH1 - 181 - 18
52DADADADAchain ggK2 - 182 - 18
62DADADADAchain hhL2 - 182 - 18
72DADADADAchain kkO2 - 182 - 18
82DADADADAchain llP2 - 182 - 18
92DTDTDADAchain ooS1 - 181 - 18
102DADADADAchain ppT2 - 182 - 18
112DTDTDADAchain ssW3 - 163 - 16
122DADADCDCchain ttX2 - 152 - 15

NCS ensembles :
ID
1
2

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Components

#1: Protein
LacI-type transcription factor


Mass: 37967.426 Da / Num. of mol.: 12
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: DNA chain
promoter DNA


Mass: 5515.591 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 10mM Tris-HCl pH 8.5, 100mM NaCl, 1mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9987 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 987667 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rsym value: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 5.2 % / Num. unique obs: 111573 / Rsym value: 1.16 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDV

7cdv


Resolution: 3.2→49.149 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 5591 5.01 %
Rwork0.2334 106017 -
obs0.2358 111608 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.43 Å2 / Biso mean: 117.3258 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.2→49.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28156 4159 0 25 32340
Biso mean---74.63 -
Num. residues----4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933408
X-RAY DIFFRACTIONf_angle_d1.64546345
X-RAY DIFFRACTIONf_chiral_restr0.0725505
X-RAY DIFFRACTIONf_plane_restr0.0085310
X-RAY DIFFRACTIONf_dihedral_angle_d18.58812161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16846X-RAY DIFFRACTION16.266TORSIONAL
12B16846X-RAY DIFFRACTION16.266TORSIONAL
13C16846X-RAY DIFFRACTION16.266TORSIONAL
14D16846X-RAY DIFFRACTION16.266TORSIONAL
15G16846X-RAY DIFFRACTION16.266TORSIONAL
16H16846X-RAY DIFFRACTION16.266TORSIONAL
17K16846X-RAY DIFFRACTION16.266TORSIONAL
18L16846X-RAY DIFFRACTION16.266TORSIONAL
19O16846X-RAY DIFFRACTION16.266TORSIONAL
110P16846X-RAY DIFFRACTION16.266TORSIONAL
111S16846X-RAY DIFFRACTION16.266TORSIONAL
112T16846X-RAY DIFFRACTION16.266TORSIONAL
21a2004X-RAY DIFFRACTION16.266TORSIONAL
22b2004X-RAY DIFFRACTION16.266TORSIONAL
23c2004X-RAY DIFFRACTION16.266TORSIONAL
24d2004X-RAY DIFFRACTION16.266TORSIONAL
25g2004X-RAY DIFFRACTION16.266TORSIONAL
26h2004X-RAY DIFFRACTION16.266TORSIONAL
27k2004X-RAY DIFFRACTION16.266TORSIONAL
28l2004X-RAY DIFFRACTION16.266TORSIONAL
29o2004X-RAY DIFFRACTION16.266TORSIONAL
210p2004X-RAY DIFFRACTION16.266TORSIONAL
211s2004X-RAY DIFFRACTION16.266TORSIONAL
212t2004X-RAY DIFFRACTION16.266TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2-3.23640.40091840.37273487
3.2364-3.27440.37252060.33833487
3.2744-3.31440.35091870.32433461
3.3144-3.35630.38131710.32173500
3.3563-3.40050.32231890.31373502
3.4005-3.4470.35661800.29933480
3.447-3.49630.34321810.30313517
3.4963-3.54840.30011930.28833473
3.5484-3.60390.32062160.27633503
3.6039-3.66290.37571520.293508
3.6629-3.72610.3231600.28183537
3.7261-3.79380.32891980.27593479
3.7938-3.86670.31281970.27733525
3.8667-3.94560.31071810.26723499
3.9456-4.03140.31141920.23853499
4.0314-4.12510.26212050.23713498
4.1251-4.22820.2811930.22893502
4.2282-4.34250.27261780.22393542
4.3425-4.47020.27871840.21973525
4.4702-4.61440.28621720.22423527
4.6144-4.77920.27661810.22443547
4.7792-4.97030.24331860.21633542
4.9703-5.19630.28331930.22813540
5.1963-5.46990.28171800.22593539
5.4699-5.81210.31311990.23853567
5.8121-6.26010.32241980.2443562
6.2601-6.88850.30451870.24153581
6.8885-7.88180.20991840.20543619
7.8818-9.91680.21281760.16533664
9.9168-49.140.22191880.18693805
Refinement TLS params.Method: refined / Origin x: 0.9602 Å / Origin y: 26.6107 Å / Origin z: -66.3359 Å
111213212223313233
T0.4432 Å20.0137 Å20.1004 Å2-0.3729 Å2-0.0286 Å2--0.4689 Å2
L0.266 °2-0.014 °20.1699 °2-0.1714 °2-0.0016 °2--0.3349 °2
S0.0343 Å °-0.0987 Å °-0.0245 Å °-0.089 Å °0.0292 Å °-0.0419 Å °0.0178 Å °-0.009 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 348
2X-RAY DIFFRACTION1allB18 - 345
3X-RAY DIFFRACTION1alla1 - 18
4X-RAY DIFFRACTION1allb1 - 18
5X-RAY DIFFRACTION1allC18 - 349
6X-RAY DIFFRACTION1allD18 - 344
7X-RAY DIFFRACTION1allc1 - 18
8X-RAY DIFFRACTION1alld1 - 18
9X-RAY DIFFRACTION1allG18 - 348
10X-RAY DIFFRACTION1allH18 - 348
11X-RAY DIFFRACTION1allg2 - 18
12X-RAY DIFFRACTION1allh2 - 18
13X-RAY DIFFRACTION1allK18 - 350
14X-RAY DIFFRACTION1allL18 - 346
15X-RAY DIFFRACTION1allk2 - 18
16X-RAY DIFFRACTION1alll2 - 18
17X-RAY DIFFRACTION1allO18 - 345
18X-RAY DIFFRACTION1allP18 - 345
19X-RAY DIFFRACTION1allo1 - 18
20X-RAY DIFFRACTION1allp2 - 18
21X-RAY DIFFRACTION1allS18 - 337
22X-RAY DIFFRACTION1allT18 - 338
23X-RAY DIFFRACTION1alls3 - 16
24X-RAY DIFFRACTION1allt2 - 15
25X-RAY DIFFRACTION1allF1 - 25

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