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- PDB-9irz: Crystal structure of YhaJ DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 9irz
TitleCrystal structure of YhaJ DNA-binding domain
ComponentsProbable HTH-type transcriptional regulator YhaJ
KeywordsTRANSCRIPTION / DNA-binding / LTTR
Function / homology
Function and homology information


positive regulation of DNA-templated transcription initiation / DNA-binding transcription activator activity / transcription cis-regulatory region binding / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Probable HTH-type transcriptional regulator YhaJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKim, M. / Kang, R. / Ryu, S.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Front Microbiol / Year: 2024
Title: High-affinity promotor binding of YhaJ mediates a low signal leakage for effective DNT detection.
Authors: Kim, M. / Kang, R. / Park, H.M. / Cho, E.B. / Lee, H.R. / Ryu, S.E.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable HTH-type transcriptional regulator YhaJ
B: Probable HTH-type transcriptional regulator YhaJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1946
Polymers22,8742
Non-polymers3204
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-37 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.157, 117.157, 35.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Probable HTH-type transcriptional regulator YhaJ


Mass: 11437.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yhaJ, b3105, JW3076 / Production host: Escherichia coli (E. coli) / References: UniProt: P67660
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-Cl pH 8.5, 2.0 M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.76→33.82 Å / Num. obs: 17579 / % possible obs: 98.86 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.97 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06215 / Rpim(I) all: 0.03468 / Rrim(I) all: 0.07136 / Net I/σ(I): 13.59
Reflection shellResolution: 1.76→1.82 Å / Rmerge(I) obs: 0.2234 / Mean I/σ(I) obs: 4.25 / Num. unique obs: 1671 / CC1/2: 0.873 / Rpim(I) all: 0.1521 / Rrim(I) all: 0.2718

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→33.82 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 2.27 / Phase error: 21.9005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 1759 10.01 %
Rwork0.1809 15818 -
obs0.1849 17577 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.53 Å2
Refinement stepCycle: LAST / Resolution: 1.76→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 16 120 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361488
X-RAY DIFFRACTIONf_angle_d0.66342003
X-RAY DIFFRACTIONf_chiral_restr0.0371236
X-RAY DIFFRACTIONf_plane_restr0.0065258
X-RAY DIFFRACTIONf_dihedral_angle_d4.4927211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.29511270.22361143X-RAY DIFFRACTION94.42
1.81-1.860.27231290.20641212X-RAY DIFFRACTION96.96
1.86-1.920.20961310.19511198X-RAY DIFFRACTION98.37
1.92-1.990.24821400.19431229X-RAY DIFFRACTION98.35
1.99-2.070.25031360.19151215X-RAY DIFFRACTION99.41
2.07-2.160.20251320.1671233X-RAY DIFFRACTION99.64
2.16-2.280.2181360.16951208X-RAY DIFFRACTION99.33
2.28-2.420.20851400.17951231X-RAY DIFFRACTION99.78
2.42-2.610.21921370.1811218X-RAY DIFFRACTION99.78
2.61-2.870.26451380.19321242X-RAY DIFFRACTION99.78
2.87-3.280.22411350.18061229X-RAY DIFFRACTION99.93
3.29-4.140.20571370.16551229X-RAY DIFFRACTION100
4.14-33.820.19691410.18111231X-RAY DIFFRACTION99.78

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