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- PDB-6p0s: Crystal structure of ternary DNA complex "FX2" containing E. coli... -

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Basic information

Entry
Database: PDB / ID: 6p0s
TitleCrystal structure of ternary DNA complex "FX2" 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: 2.7 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
A: DNA-binding protein Fis
B: 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)45,8855
Polymers45,8855
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-69 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.670, 107.670, 150.430
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: 8275.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (27-MER), FX1-2


Mass: 8310.391 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 5.14 Å3/Da / Density % sol: 76.08 %
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: 0.9717 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: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.7→87.55 Å / Num. obs: 23763 / % possible obs: 95.6 % / Redundancy: 9.347 % / Biso Wilson estimate: 90.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.121 / Χ2: 0.947 / Net I/σ(I): 12.53 / Num. measured all: 222119 / Scaling rejects: 6924
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
2.7-2.776.570.4923.7310039179515280.9150.53485.1
2.77-2.856.6090.4294.3910131175215330.9180.46687.5
2.85-2.937.2780.3815.1911310172115540.9360.41190.3
2.93-3.027.2550.3216.1110897165715020.950.34690.6
3.02-3.127.4030.2537.7111200161215130.970.27293.9
3.12-3.237.8390.1889.9411805155915060.9820.20196.6
3.23-3.358.6410.15912.0212737150814740.9910.16997.7
3.35-3.499.1020.14913.4513007145914290.9890.15797.9
3.49-3.658.9880.14113.7912466140513870.9890.14998.7
3.65-3.8210.2010.1315.3313588134313320.9930.13699.2
3.82-4.0311.140.12716.6114203128312750.9930.13299.4
4.03-4.2811.70.11517.914145121612090.9940.1299.4
4.28-4.5712.0180.11118.6113700114711400.9940.11599.4
4.57-4.9411.7370.10718.3812641107810770.9930.11299.9
4.94-5.4110.6750.10317.61106009969930.9940.10899.7
5.41-6.0512.1660.09819.17110109119050.9940.10299.3
6.05-6.9812.40.08919.1699708088040.9970.09399.5
6.98-8.5512.3160.07919.7986097026990.9970.08299.6
8.55-12.0910.9020.07918.8161055605600.9950.083100
12.09-87.5511.5340.12319.3439563433430.9980.13100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å87.44 Å
Translation2.8 Å87.44 Å

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASER1.3.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P0T

6p0t


Resolution: 2.7→87.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1145 4.82 %RANDOM
Rwork0.222 ---
obs0.222 23762 95.6 %-
Displacement parametersBiso max: 173.01 Å2 / Biso mean: 74.42 Å2 / Biso min: 18.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.8663 Å20 Å20 Å2
2--0.8663 Å20 Å2
3----1.7326 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.7→87.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 1101 0 58 2886
Biso mean---52.16 -
Num. residues----271
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d915SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes349HARMONIC5
X-RAY DIFFRACTIONt_it2992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3080SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2992HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4268HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.21
LS refinement shellResolution: 2.7→2.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3728 25 5.25 %
Rwork0.4363 451 -
all0.4329 476 -
obs--82.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.18912.16770.79023.0101-0.1323.5339-0.09680.7610.2156-0.33290.0616-0.2014-0.39160.64180.03520.0751-0.1435-0.02320.03950.0745-0.194816.5642-32.8865-11.5002
27.09353.25032.78293.26161.88514.884-0.06910.7262-0.0876-0.14920.0502-0.4736-0.27210.91610.0188-0.0579-0.1931-0.00950.17480.1082-0.148725.3158-33.5513-8.8012
32.03481.2982-0.24562.1162-0.77171.68670.0238-0.97440.2567-0.0632-0.38360.0342-0.42560.10040.3598-0.0257-0.1844-0.06780.00650.0119-0.117215.53-31.77357.9788
41.6641-0.1797-0.55561.1483-1.05932.01570.0427-0.83260.48470.0664-0.34060.0142-0.44790.22090.2978-0.0025-0.1941-0.0955-0.06330.0169-0.139315.8561-32.61478.1982
54.1369-1.34631.95156.6693-0.63897.44150.1323-0.1857-0.45330.06750.03960.58420.50750.0369-0.17190.0768-0.1026-0.0104-0.01080.0897-0.02451.1422-54.23388.6867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A8 - 98
2X-RAY DIFFRACTION2{ B|* }B9 - 98
3X-RAY DIFFRACTION3{ C|* }C1 - 27
4X-RAY DIFFRACTION4{ D|* }D1 - 27
5X-RAY DIFFRACTION5{ E|* }E1 - 52

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