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- PDB-6p0t: Crystal structure of ternary DNA complex "FX(1-2)-1Xis" containin... -

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Basic information

Entry
Database: PDB / ID: 6p0t
TitleCrystal structure of ternary DNA complex "FX(1-2)-1Xis" containing E. coli Fis and phage lambda Xis
Components
  • (DNA (27-MER), FX1-2) x 2
  • DNA-binding protein Fis
  • Excisionase
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA ternary complex / DNA shape / cooperative binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription activator activity / DNA-binding transcription repressor activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription activator activity / DNA-binding transcription repressor activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex / response to radiation / nucleosome / DNA recombination / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / cytosol
Similarity search - Function
Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / DNA-binding protein Fis / : / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Putative DNA-binding domain superfamily ...Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / DNA-binding protein Fis / : / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Putative DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Excisionase / DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.603 Å
AuthorsHancock, S.P. / Cascio, D. / Johnson, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM038509 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Cooperative DNA binding by proteins through DNA shape complementarity.
Authors: Hancock, S.P. / Cascio, D. / Johnson, R.C.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: DNA-binding protein Fis
A: DNA-binding protein Fis
C: DNA (27-MER), FX1-2
D: DNA (27-MER), FX1-2
E: Excisionase


Theoretical massNumber of molelcules
Total (without water)45,8865
Polymers45,8865
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-68 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.190, 108.190, 152.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA-binding protein Fis / Factor-for-inversion stimulation protein / Hin recombinational enhancer-binding protein


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fis, b3261, JW3229 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6R3
#2: DNA chain DNA (27-MER), FX1-2


Mass: 8295.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (27-MER), FX1-2


Mass: 8291.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein Excisionase


Mass: 6793.799 Da / Num. of mol.: 1 / Fragment: residues 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: xis / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03699

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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: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→88.255 Å / Num. obs: 10977 / % possible obs: 99.8 % / Redundancy: 12.755 % / Biso Wilson estimate: 114.593 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.123 / Χ2: 0.936 / Net I/σ(I): 13.14 / Num. measured all: 140007 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.6-3.712.6970.8163.0995617757530.8480.8597.2
3.7-3.813.3390.6374.13102717707700.930.662100
3.8-3.9113.1340.5664.6799827607600.9310.588100
3.91-4.0312.8220.4335.9895787477470.960.451100
4.03-4.1611.8340.3277.3884147117110.9720.341100
4.16-4.3113.540.2539.5890586696690.9850.263100
4.31-4.4713.5850.23110.6591706756750.9880.24100
4.47-4.6513.3790.18612.3285496396390.9920.193100
4.65-4.8613.2680.17413.0281606156150.9920.181100
4.86-5.112.8920.16214.2377746036030.9920.169100
5.1-5.3712.360.14715.1869345615610.990.154100
5.37-5.712.2590.12816.6967795535530.9940.134100
5.7-6.0913.4080.12218.5267315025020.9940.127100
6.09-6.5813.0360.11519.4161794744740.9960.119100
6.58-7.2112.6040.09820.5157604574570.9960.102100
7.21-8.0611.4410.0824.1945423973970.9960.084100
8.06-9.312.2350.06728.244173613610.9970.07100
9.3-11.3912.1240.06430.9438073143140.9970.067100
11.39-16.1110.5880.06529.327002552550.9950.068100
16.11-88.25510.1930.05529.9416411611610.9990.058100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.4 Å88.11 Å
Translation7.4 Å88.11 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.6.1phasing
PHENIX(1.15_3459)refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P0U

6p0u


Resolution: 3.603→88.255 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 561 5.11 %
Rwork0.1993 10413 -
obs0.2017 10974 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.22 Å2 / Biso mean: 122.2536 Å2 / Biso min: 73.81 Å2
Refinement stepCycle: final / Resolution: 3.603→88.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 1101 0 0 2800
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6031-3.96570.31911380.26142502264099
3.9657-4.53950.22681190.21725862705100
4.5395-5.71920.24841530.201925822735100
5.7192-88.28140.23921510.178727432894100
Refinement TLS params.Method: refined / Origin x: 36.7742 Å / Origin y: -16.2079 Å / Origin z: -0.0044 Å
111213212223313233
T0.8765 Å2-0.1055 Å20.078 Å2-0.9284 Å2-0.0629 Å2--1.0297 Å2
L1.7135 °20.5005 °2-0.3471 °2-2.0898 °20.3242 °2--1.3399 °2
S-0.1117 Å °0.0608 Å °0.0234 Å °-0.1651 Å °-0.119 Å °0.3805 Å °0.1372 Å °-0.2625 Å °0.2611 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB8 - 98
2X-RAY DIFFRACTION1allA8 - 98
3X-RAY DIFFRACTION1allC1 - 27
4X-RAY DIFFRACTION1allD1 - 27
5X-RAY DIFFRACTION1allE1 - 52

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