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- PDB-7t5w: Structure of E. coli CapH C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7t5w
TitleStructure of E. coli CapH C-terminal domain
ComponentsHelix-turn-helix domain-containing protein
KeywordsDNA BINDING PROTEIN / helix turn helix / HTH / DdrO
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Helix-turn-helix domain / : / 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
Similarity search - Domain/homology
Helix-turn-helix domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLau, R.K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI148814 United States
CitationJournal: Embo J. / Year: 2022
Title: A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage.
Authors: Lau, R.K. / Enustun, E. / Gu, Y. / Nguyen, J.V. / Corbett, K.D.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 2023Group: 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: Helix-turn-helix domain-containing protein
B: Helix-turn-helix domain-containing protein
C: Helix-turn-helix domain-containing protein
D: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)21,1114
Polymers21,1114
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-42 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.023, 39.855, 46.256
Angle α, β, γ (deg.)90.000, 98.731, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide
Helix-turn-helix domain-containing protein / Helix-turn-helix transcriptional regulator / Transcriptional regulator / XRE family transcriptional regulator


Mass: 5277.855 Da / Num. of mol.: 4 / Fragment: C-terminal residues 67-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nadR_1, BHS87_27750, D9K17_19515, GRQ19_13110, HV109_14215, NCTC13216_00230
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X1LKI5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.9 Å3/Da / Density % sol: 35.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate pH 3.0, 1.6 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 15936 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.13 Å2 / CC1/2: 1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.07 / Net I/σ(I): 26.2
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 768 / CC1/2: 0.631 / Rpim(I) all: 0.45 / Rrim(I) all: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7T5V

7t5v


Resolution: 1.75→45.72 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 709 4.45 %
Rwork0.2098 15208 -
obs0.2112 15917 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 60 1319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011283
X-RAY DIFFRACTIONf_angle_d1.00121715
X-RAY DIFFRACTIONf_chiral_restr0.0462174
X-RAY DIFFRACTIONf_plane_restr0.0096230
X-RAY DIFFRACTIONf_dihedral_angle_d12.5979503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.890.31231390.28612900X-RAY DIFFRACTION95.51
1.89-2.080.25621270.2113064X-RAY DIFFRACTION99.59
2.08-2.380.23241370.20853050X-RAY DIFFRACTION99.41
2.38-30.22641330.22363078X-RAY DIFFRACTION99.69
3-45.720.23421730.19783116X-RAY DIFFRACTION99.43
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)
11.50649018205-0.4910321666670.3039759437840.956227011017-0.1360685039961.99782470814-0.0150665750004-0.159566548137-0.0690985061680.03549040623540.02355961136020.08465948200370.0347429615403-0.126931896856-1.05493456726E-50.234844743317-0.007332537567820.005201596941930.225323996987-0.003633387546860.2435719865174.190158652091.7236572010710.3676971791
22.42695069196-0.55059129647-1.185377644851.537705124410.961640786913.206243132280.0965855391840.2760771953420.00566095482881-0.145675102813-0.0490948917687-0.0278914367803-0.220179501493-0.07094435054080.005166976257860.2556293325910.039768982225-0.007899182550310.2614502735670.01470609553020.24838100426816.678311882-0.432285513735-10.2331072614
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A or chain BA - BA - B70 - 1051 - 41
22chain C or chain DC - DC - D67 - 1061 - 37

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