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- PDB-5k5r: AspA-32mer DNA,crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 5k5r
TitleAspA-32mer DNA,crystal form 2
Components
  • (DNA (32-MER)) x 2
  • AspA
KeywordsTRANSCRIPTION/DNA / AspA / centromere / DNA / partition / archaea / 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
PHOSPHATE ION / DNA / DNA (> 10) / HTH arsR-type domain-containing protein
Similarity search - Component
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsSchumacher, M.
CitationJournal: 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
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Other
SupersessionSep 27, 2023ID: 4RU7
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_PDB_obs_spr / pdbx_initial_refinement_model / 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 (32-MER)
N: DNA (32-MER)
E: AspA
F: AspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,08317
Polymers88,2288
Non-polymers8559
Water00
1
C: AspA
D: AspA
A: AspA
B: AspA
P: DNA (32-MER)
N: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6639
Polymers65,3786
Non-polymers2853
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: AspA
F: AspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4208
Polymers22,8502
Non-polymers5706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.240, 55.880, 101.620
Angle α, β, γ (deg.)90.000, 110.500, 90.000
Int Tables number5
Space group name H-MC121
DetailsProtein binds to DNA in dimer-of-dimer form, and extends to superhelix.

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Components

#1: Protein
AspA


Mass: 11425.244 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 (32-MER)


Mass: 9845.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (32-MER)


Mass: 9831.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 200, phosphate/citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→48.974 Å / Num. obs: 14275 / % possible obs: 96.69 % / Redundancy: 4 % / Rsym value: 0.076 / Net I/σ(I): 6
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.384

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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: 4RS8

4rs8


Resolution: 3.09→48.974 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.93
RfactorNum. reflection% reflection
Rfree0.2749 1428 10 %
Rwork0.2015 --
obs0.2089 14275 96.69 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 55.568 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 176.89 Å2 / Biso mean: 88.83 Å2 / Biso min: 29.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.7818 Å2-0 Å2-4.5574 Å2
2---20.4401 Å2-0 Å2
3---23.2219 Å2
Refinement stepCycle: final / Resolution: 3.09→48.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 1306 45 0 5784
Biso mean--126.3 --
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025999
X-RAY DIFFRACTIONf_angle_d0.7148375
X-RAY DIFFRACTIONf_chiral_restr0.045966
X-RAY DIFFRACTIONf_plane_restr0.002804
X-RAY DIFFRACTIONf_dihedral_angle_d23.3252367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0901-3.20050.42921230.31751106122984
3.2005-3.32860.38861410.26981270141197
3.3286-3.48010.3171450.24411306145199
3.4801-3.66350.35051440.23341287143199
3.6635-3.89290.32351440.22551304144899
3.8929-4.19340.25151470.19571315146299
4.1934-4.61510.24511450.18041306145199
4.6151-5.28220.27511460.17711315146198
5.2822-6.65240.26151450.20281314145997
6.6524-48.98010.21721480.16881324147295

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