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- PDB-5kk1: Structure of pNOB8 AspA-DNA complex. -

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Basic information

Entry
Database: PDB / ID: 5kk1
TitleStructure of pNOB8 AspA-DNA complex.
Components
  • (DNA (31-MER)) x 2
  • AspA
KeywordsTRANSCRIPTION/DNA / AspA / partition / segregation / pNOB8 / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / identical protein binding
Similarity search - Function
Winged helix DNA-binding domain / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Winged helix DNA-binding domain / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH arsR-type domain-containing protein
Similarity search - Component
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.38 Å
AuthorsSchumacher, M.
Citation
Journal: To Be Published
Title: to be published
Authors: Schumacher, M.
#1: Journal: Science / Year: 2015
Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: AspA
D: AspA
A: AspA
B: AspA
P: DNA (31-MER)
N: DNA (31-MER)
E: AspA
F: AspA


Theoretical massNumber of molelcules
Total (without water)82,6378
Polymers82,6378
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-161 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.516, 55.927, 99.964
Angle α, β, γ (deg.)90.000, 109.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
AspA


Mass: 10596.363 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. NOB8H2 (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: O93706
#2: DNA chain DNA (31-MER)


Mass: 9516.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (31-MER)


Mass: 9542.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG 550, MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.38→51.935 Å / Num. obs: 9960 / % possible obs: 90 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.9
Reflection shellResolution: 3.38→3.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 4.4 / % possible all: 84.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5Q

5k5q


Resolution: 3.38→51.935 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.2455 995 10.02 %
Rwork0.2156 --
obs0.2186 9930 89.44 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 48.03 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 182.24 Å2 / Biso mean: 77.58 Å2 / Biso min: 28.11 Å2
Baniso -1Baniso -2Baniso -3
1-24.0799 Å2-0 Å210.9214 Å2
2---3.2593 Å20 Å2
3----20.8207 Å2
Refinement stepCycle: final / Resolution: 3.38→51.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4431 1265 0 0 5696
Num. residues----607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055915
X-RAY DIFFRACTIONf_angle_d0.7248248
X-RAY DIFFRACTIONf_chiral_restr0.039959
X-RAY DIFFRACTIONf_plane_restr0.005801
X-RAY DIFFRACTIONf_dihedral_angle_d22.2392345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3803-3.55840.33911300.26711167129782
3.5584-3.78130.31841480.2631323147194
3.7813-4.07320.24621430.22221288143193
4.0732-4.48290.24851460.19191307145392
4.4829-5.13110.2071440.20091298144290
5.1311-6.46270.26521410.22671274141589
6.4627-51.94070.1941430.19161278142186

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