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- PDB-7t5v: Structure of E. coli CapH C-terminal domain I99M mutant -

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Basic information

Entry
Database: PDB / ID: 7t5v
TitleStructure of E. coli CapH C-terminal domain I99M mutant
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: 1.26 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 1.3Apr 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: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)5,2961
Polymers5,2961
Non-polymers00
Water82946
1
A: Helix-turn-helix domain-containing protein

A: Helix-turn-helix domain-containing protein


Theoretical massNumber of molelcules
Total (without water)10,5922
Polymers10,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1810 Å2
ΔGint-18 kcal/mol
Surface area5310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.383, 38.383, 59.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

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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: 5295.893 Da / Num. of mol.: 1 / Fragment: C-terminal residues 67-107 / Mutation: I99M
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.: 46 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25 mM MgCl2, 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.26→59.43 Å / Num. obs: 12610 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Net I/σ(I): 21.1
Reflection shellResolution: 1.26→1.28 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2 / Num. unique obs: 597 / CC1/2: 0.83 / Rpim(I) all: 0.46 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal alpha helix

Resolution: 1.26→32.24 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 27.0136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 594 4.73 %
Rwork0.1913 11966 -
obs0.1924 12560 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.14 Å2
Refinement stepCycle: LAST / Resolution: 1.26→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms294 0 0 46 340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0107306
X-RAY DIFFRACTIONf_angle_d0.8959407
X-RAY DIFFRACTIONf_chiral_restr0.06839
X-RAY DIFFRACTIONf_plane_restr0.009354
X-RAY DIFFRACTIONf_dihedral_angle_d17.4423124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.390.24191370.2252924X-RAY DIFFRACTION99.58
1.39-1.590.25221500.18792928X-RAY DIFFRACTION99.97
1.59-20.21541570.20122973X-RAY DIFFRACTION99.87
2-32.240.20751500.18743141X-RAY DIFFRACTION99.43

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