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- PDB-7t8i: Crystal structure of the ImmR transcriptional regulator DNA-bindi... -

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Basic information

Entry
Database: PDB / ID: 7t8i
TitleCrystal structure of the ImmR transcriptional regulator DNA-binding domain of Bacillus subtilis
Components(Phage element (ICEBs1)transcriptional regulator (Xre family)) x 2
KeywordsDNA BINDING PROTEIN / HTH-DNA binding domain / dimerisation / immunity repressor protein / bacterial infection / horizontal gene transfer
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Phage element (ICEBs1)transcriptional regulator (Xre family)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCaliandro, R. / de Diego, I. / Gomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2022
Title: Crystal structure report of the ImmR transcriptional regulator DNA-binding domain of the Bacillus subtilis ICEBs1 transposon.
Authors: Caliandro, R. / de Diego, I. / Gomis-Ruth, F.X.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Apr 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.3Apr 13, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage element (ICEBs1)transcriptional regulator (Xre family)
B: Phage element (ICEBs1)transcriptional regulator (Xre family)


Theoretical massNumber of molelcules
Total (without water)14,9982
Polymers14,9982
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.033, 48.340, 64.460
Angle α, β, γ (deg.)90.000, 97.474, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 18 or resid 20...
d_2ens_1(chain "B" and (resid 0 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLNA1 - 19
d_12ens_1GLUASNA21 - 27
d_13ens_1GLYTYRA29 - 40
d_14ens_1ASPLYSA42 - 50
d_15ens_1SERLYSA52 - 65
d_21ens_1ALAGLNB1 - 19
d_22ens_1GLUASNB21 - 27
d_23ens_1GLYTYRB29 - 40
d_24ens_1ASPLYSB42 - 50
d_25ens_1SERLYSB52 - 65

NCS oper: (Code: givenMatrix: (-0.999954986145, -0.00901027934436, -0.00297330607399), (0.00901936055168, -0.999954657711, -0.00305510351193), (-0.00294564392142, -0.00308178330946, 0.999990912855) ...NCS oper: (Code: given
Matrix: (-0.999954986145, -0.00901027934436, -0.00297330607399), (0.00901936055168, -0.999954657711, -0.00305510351193), (-0.00294564392142, -0.00308178330946, 0.999990912855)
Vector: -4.21884563794, -5.27339386578, -0.0573595182652)

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Components

#1: Protein Phage element (ICEBs1)transcriptional regulator (Xre family) / Transcriptional regulator Cro/CI family


Mass: 7505.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues G-A are left over from the expression tag.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_4397, SC09_Contig25orf00616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1M9H4
#2: Protein Phage element (ICEBs1)transcriptional regulator (Xre family) / Transcriptional regulator Cro/CI family


Mass: 7492.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues G-A are left over from the expression tag.
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_4397, SC09_Contig25orf00616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1M9H4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Suitable crystals of ImmR-DBD were obtained with 18%(w) PEG 3350, 10 mM magnesium chloride, 50 mM Tris-HCl pH 8.5 as reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→43.97 Å / Num. obs: 9322 / % possible obs: 94 % / Redundancy: 2.8 % / Biso Wilson estimate: 5.8 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.186 / Net I/σ(I): 3.3
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 464 / CC1/2: 0.591 / Rpim(I) all: 0.433 / % possible all: 71.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
iMOSFLMdata reduction
PHASERphasing
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.1→43.97 Å / SU ML: 0.4141 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3464 454 4.87 %
Rwork0.2588 8867 -
obs0.2631 9321 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 142 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01381074
X-RAY DIFFRACTIONf_angle_d1.2931444
X-RAY DIFFRACTIONf_chiral_restr0.0645159
X-RAY DIFFRACTIONf_plane_restr0.0114188
X-RAY DIFFRACTIONf_dihedral_angle_d16.0348433
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.786370242233 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40.36981310.25752680X-RAY DIFFRACTION87.22
2.4-3.030.34521480.25783079X-RAY DIFFRACTION99.54
3.03-43.970.33551750.26013108X-RAY DIFFRACTION99.82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.140038169087-0.04662296826760.07519922459210.0631988002924-0.05122274031510.1317331236420.06285903176840.0423695452061-0.0837269606267-0.03797364240610.0006661582389860.0241618914440.0632420184595-0.002646561568560.287243374380.05846009946770.0195650047062-0.02631056048450.0412840909676-0.006417062031970.05382403057766.33735531576-10.399313212310.8067341382
20.007273222387610.008318214182570.01870058810050.01205309466230.01246760616470.08311071943070.0338976706665-0.01185568869510.0761943643792-0.002649012987580.0250805688805-0.00324256375447-0.04068192495760.01084885379870.1924419279150.05728740547830.03044925492630.02581719733770.0802956942051-2.43206842523E-50.0773705126759-10.41422875465.0032121816510.6837887262
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 0 - 64 / Label seq-ID: 1 - 65

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' )AA
22(chain 'B' )BB

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