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- PDB-5k5q: Structure of AspA-DNA complex: novel centromere bindng protein-ce... -

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Basic information

Entry
Database: PDB / ID: 5k5q
TitleStructure of AspA-DNA complex: novel centromere bindng protein-centromere complex
Components
  • (DNA (32-MER)) x 2
  • AspA
KeywordsTRANSCRIPTION/DNA / AspA / centromere / segregation / archaea / 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
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: 2.649 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
SupersessionJun 1, 2016ID: 4RSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Structure summary
Revision 1.2Sep 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_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)83,44410
Polymers83,2548
Non-polymers1902
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23490 Å2
ΔGint-179 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.650, 56.920, 103.800
Angle α, β, γ (deg.)90.000, 112.300, 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 (32-MER)


Mass: 9829.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (32-MER)


Mass: 9846.403 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.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG 3000, 0.1 M sodium phosphate/citrate pH 6.2

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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: 2.649→48.018 Å / Num. obs: 22831 / % possible obs: 92.64 % / Redundancy: 4 % / Rsym value: 0.058 / Net I/σ(I): 8.5

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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: 2.649→48.018 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.32
RfactorNum. reflection% reflection
Rfree0.2795 1991 8.72 %
Rwork0.2598 --
obs0.2615 22831 92.64 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 60.354 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 174.12 Å2 / Biso mean: 100.29 Å2 / Biso min: 34.79 Å2
Baniso -1Baniso -2Baniso -3
1-20.7114 Å2-0 Å235.1093 Å2
2---5.2885 Å20 Å2
3----15.4229 Å2
Refinement stepCycle: final / Resolution: 2.649→48.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 1306 15 0 5754
Biso mean--118.05 --
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035971
X-RAY DIFFRACTIONf_angle_d0.7538333
X-RAY DIFFRACTIONf_chiral_restr0.041966
X-RAY DIFFRACTIONf_plane_restr0.002804
X-RAY DIFFRACTIONf_dihedral_angle_d23.3362367
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 (%)
2.6493-2.7440.50381540.44661610176471
2.744-2.85390.42051750.3851822199783
2.8539-2.98370.40052010.3762129233095
2.9837-3.1410.43822070.32622195240298
3.141-3.33780.32722090.28942142235196
3.3378-3.59540.33482070.26742183239097
3.5954-3.95710.28772090.26922179238897
3.9571-4.52930.24952090.23192192240197
4.5293-5.70490.2482110.23522202241397
5.7049-48.02620.21762090.22942186239594

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