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- PDB-5k1y: P2(1) Structure of pNOB8 AspA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5k1y
TitleP2(1) Structure of pNOB8 AspA-DNA complex
Components
  • (DNA (33-MER)) x 2
  • AspA
KeywordsTRANSCRIPTION/DNA / AspA / DNA / pNOB8 / segregation / TRANSCRIPTION - DNA complex / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.97 Å
AuthorsSchumacher, M.
CitationJournal: To Be Published
Title: Detailed structural analysis of AspA-DNA contacts
Authors: Schumacher, M.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2016ID: 4RU7, 5FC0
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Other
Revision 1.2Feb 6, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (33-MER)
N: DNA (33-MER)
E: AspA
F: AspA


Theoretical massNumber of molelcules
Total (without water)83,7968
Polymers83,7968
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23290 Å2
ΔGint-171 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.366, 72.306, 90.508
Angle α, β, γ (deg.)90.000, 114.720, 90.000
Int Tables number4
Space group name H-MP1211

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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 (33-MER)


Mass: 10040.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (33-MER)


Mass: 10177.583 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG, phosphate/citrate pH 4.2

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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: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→39.461 Å / Num. obs: 18451 / % possible obs: 89.26 % / Redundancy: 1.8 % / Net I/σ(I): 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 / Resolution: 2.97→39.461 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.01
RfactorNum. reflection% reflection
Rfree0.2796 1827 9.9 %
Rwork0.2097 --
obs0.2168 18451 89.26 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 68.388 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 210.69 Å2 / Biso mean: 97.08 Å2 / Biso min: 45.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.1069 Å2-0 Å219.426 Å2
2---11.4086 Å2-0 Å2
3---13.5155 Å2
Refinement stepCycle: final / Resolution: 2.97→39.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 1341 0 0 5775
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046002
X-RAY DIFFRACTIONf_angle_d0.8728380
X-RAY DIFFRACTIONf_chiral_restr0.048975
X-RAY DIFFRACTIONf_plane_restr0.003806
X-RAY DIFFRACTIONf_dihedral_angle_d23.022387
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 (%)
2.9701-3.07620.42821160.3126993110954
3.0762-3.19930.35451330.24311219135265
3.1993-3.34490.34441510.25011452160378
3.3449-3.52110.33321890.2391804199398
3.5211-3.74160.30822150.241118352050100
3.7416-4.03020.33152050.228718492054100
4.0302-4.43530.30551970.200718812078100
4.4353-5.07590.25212100.196718442054100
5.0759-6.39080.2592060.200118782084100
6.3908-39.46440.23582050.19211869207497

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