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- PDB-7cx5: Crystal structure of the DNA-binding domain of Bacillus subtilis CssR -

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Basic information

Entry
Database: PDB / ID: 7cx5
TitleCrystal structure of the DNA-binding domain of Bacillus subtilis CssR
ComponentsTranscriptional regulatory protein CssR
KeywordsDNA BINDING PROTEIN / two-component system / response regulator / DNA binding domain / envelope stress
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulatory protein CssR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.07 Å
AuthorsDahal, P. / Kim, D.Y. / Kwon, E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the DNA-binding domain of Bacillus subtilis CssR.
Authors: Dahal, P. / Kim, D.Y. / Kwon, E.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Transcriptional regulatory protein CssR


Theoretical massNumber of molelcules
Total (without water)11,1561
Polymers11,1561
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5590 Å2
Unit cell
Length a, b, c (Å)29.410, 52.740, 58.990
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 Transcriptional regulatory protein CssR


Mass: 11155.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: cssR, BSU33010 / Plasmid: pETDeut-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32192
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 2 M Lithium sulfate, 2% (v/v) PEG400, and 0.1 M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.07→39.32 Å / Num. obs: 41035 / % possible obs: 98.5 % / Redundancy: 5.75 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.6
Reflection shellResolution: 1.07→1.08 Å / Rmerge(I) obs: 0.655 / Num. unique obs: 2021

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.07→39.32 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 2040 4.98 %
Rwork0.1944 38933 -
obs0.1949 40973 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.28 Å2 / Biso mean: 12.3468 Å2 / Biso min: 4.97 Å2
Refinement stepCycle: final / Resolution: 1.07→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 0 137 882
Biso mean---20.9 -
Num. residues----88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.07-1.090.3511210.35312559268098
1.09-1.120.37921460.29412557270398
1.12-1.150.2591420.2492510265298
1.15-1.180.21751410.2182606274799
1.18-1.220.19641440.20412568271299
1.22-1.260.20311410.1862560270199
1.26-1.310.20021270.17882586271398
1.31-1.370.19791380.18042582272099
1.37-1.450.19691350.17642574270998
1.45-1.540.19591320.17062597272998
1.54-1.660.17591200.172599271998
1.66-1.820.1951400.1762615275599
1.82-2.090.19021290.18392639276898
2.09-2.630.19111420.18782640278298
2.63-39.320.20031420.19962741288397
Refinement TLS params.Method: refined / Origin x: 10.9 Å / Origin y: 4.209 Å / Origin z: 8.6359 Å
111213212223313233
T0.0616 Å20.0053 Å20.0041 Å2-0.0578 Å20.0037 Å2--0.0573 Å2
L0.3109 °2-0.0402 °20.1213 °2-0.2153 °2-0.1453 °2--0.44 °2
S-0.0011 Å °-0.0179 Å °-0.0187 Å °-0.0023 Å °-0.0129 Å °0.0343 Å °0.0481 Å °0.0189 Å °-0.0072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA136 - 223
2X-RAY DIFFRACTION1allS1 - 137

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