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- PDB-8hnp: Archaeal transcription factor Mutant -

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Basic information

Entry
Database: PDB / ID: 8hnp
TitleArchaeal transcription factor Mutant
ComponentsArchaeal transcription regulator
KeywordsTRANSCRIPTION / Hyperthermophile / Archaeal transcription factor / Tfx
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
DNA-binding protein Tfx, archaea / DNA-binding protein Tfx, euryarchaeota / DNA binding protein Tfx, C-terminal / DNA-binding protein Tfx superfamily, archaea / DNA_binding protein, TFX, C-term / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / RNA polymerase sigma-70 region 4 / Sigma-70, region 4
Similarity search - Domain/homology
Archaeal transcription regulator
Similarity search - Component
Biological speciesThermococcus onnurineus NA1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsBae, D.W. / Cha, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: An archaeal transcription factor EnfR with a novel 'eighth note' fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA1.
Authors: Bae, D.W. / Lee, S.H. / Park, J.H. / Son, S.Y. / Lin, Y. / Lee, J.H. / Jang, B.R. / Lee, K.H. / Lee, Y.H. / Lee, H.S. / Kang, S.G. / Kim, B.S. / Cha, S.S.
History
DepositionDec 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Oct 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaeal transcription regulator
B: Archaeal transcription regulator


Theoretical massNumber of molelcules
Total (without water)35,4232
Polymers35,4232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-22 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.170, 123.170, 82.650
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

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Components

#1: Protein Archaeal transcription regulator


Mass: 17711.488 Da / Num. of mol.: 2 / Mutation: T55I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus NA1 (archaea) / Gene: TON_1525 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTS4

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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: 4.42 Å3/Da / Density % sol: 76.29 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 30% PEG 400, 100 mM HEPES pH 7.5, and 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 14609 / % possible obs: 86.9 % / Redundancy: 4.02 % / Biso Wilson estimate: 123 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.86
Reflection shellResolution: 3.39→3.48 Å / Num. unique obs: 1065 / CC1/2: 0.909 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.39→45.84 Å / SU ML: 0.518 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.8581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2753 1461 10.01 %
Rwork0.2357 13140 -
obs0.2395 14601 86.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.64 Å2
Refinement stepCycle: LAST / Resolution: 3.39→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 0 0 2127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172152
X-RAY DIFFRACTIONf_angle_d0.42512914
X-RAY DIFFRACTIONf_chiral_restr0.0374358
X-RAY DIFFRACTIONf_plane_restr0.0024373
X-RAY DIFFRACTIONf_dihedral_angle_d21.1515785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.39-3.510.41381460.33921309X-RAY DIFFRACTION86.61
3.52-3.660.36121520.30881331X-RAY DIFFRACTION89.02
3.66-3.820.36241530.26911367X-RAY DIFFRACTION89.25
3.82-4.020.27211490.26511319X-RAY DIFFRACTION87.9
4.02-4.270.241420.23741331X-RAY DIFFRACTION87.94
4.28-4.60.25291520.23331314X-RAY DIFFRACTION86.9
4.61-5.070.2561440.23451302X-RAY DIFFRACTION86.38
5.07-5.80.29341470.24841299X-RAY DIFFRACTION86.12
5.8-7.30.30741440.26251303X-RAY DIFFRACTION85.42
7.31-45.840.22881320.18231265X-RAY DIFFRACTION83.2

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