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- PDB-8hno: Archaeal transcription factor Wild type -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8hno
TitleArchaeal transcription factor Wild type
ComponentsArchaeal transcription regulator
KeywordsTRANSCRIPTION / Hyperthermophile / 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: 2.84 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3992
Polymers35,3992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-20 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.686, 102.686, 90.386
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU(chain 'A' and (resid 4 through 22 or resid 24...AA4 - 224 - 22
12GLNGLNLEULEU(chain 'A' and (resid 4 through 22 or resid 24...AA24 - 9024 - 90
13ILEILEILEILE(chain 'A' and (resid 4 through 22 or resid 24...AA92 - 11192 - 111
14ASPASPILEILE(chain 'A' and (resid 4 through 22 or resid 24...AA113 - 115113 - 115
15ARGARGASPASP(chain 'A' and (resid 4 through 22 or resid 24...AA118 - 125118 - 125
16ASPASPGLUGLU(chain 'A' and (resid 4 through 22 or resid 24...AA128 - 139128 - 139
27LYSLYSLEULEU(chain 'B' and (resid 4 through 22 or resid 24...BB4 - 224 - 22
28GLNGLNLEULEU(chain 'B' and (resid 4 through 22 or resid 24...BB24 - 9024 - 90
29ILEILEILEILE(chain 'B' and (resid 4 through 22 or resid 24...BB92 - 11192 - 111
210ASPASPILEILE(chain 'B' and (resid 4 through 22 or resid 24...BB113 - 115113 - 115
211ARGARGASPASP(chain 'B' and (resid 4 through 22 or resid 24...BB118 - 125118 - 125
212ASPASPGLUGLU(chain 'B' and (resid 4 through 22 or resid 24...BB128 - 139128 - 139

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Components

#1: Protein Archaeal transcription regulator


Mass: 17699.434 Da / Num. of mol.: 2
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: 3.37 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 30% polyethylene glycol (PEG) 400, 100 mM HEPES pH 7.5, and 200 mM sodium chloride

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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: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 11845 / % possible obs: 98.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 63.99 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.571
Reflection shellResolution: 2.84→2.89 Å / Rmerge(I) obs: 0.414 / Num. unique obs: 545 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→45.92 Å / SU ML: 0.3793 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 25.1944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 618 5.23 %
Rwork0.2215 11206 -
obs0.2228 11824 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.18 Å2
Refinement stepCycle: LAST / Resolution: 2.84→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 0 0 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942244
X-RAY DIFFRACTIONf_angle_d1.09683018
X-RAY DIFFRACTIONf_chiral_restr0.0537359
X-RAY DIFFRACTIONf_plane_restr0.0063384
X-RAY DIFFRACTIONf_dihedral_angle_d19.3998873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.120.34681420.32042718X-RAY DIFFRACTION98.21
3.12-3.570.29811570.27262749X-RAY DIFFRACTION99.28
3.57-4.50.26941450.20892803X-RAY DIFFRACTION99.26
4.5-45.920.19111740.18452936X-RAY DIFFRACTION99.42

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