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- PDB-5ds9: Crystal structure of Fis bound to 27bp DNA F1-8A (AAATTAGTTTGAATT... -

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Basic information

Entry
Database: PDB / ID: 5ds9
TitleCrystal structure of Fis bound to 27bp DNA F1-8A (AAATTAGTTTGAATTTTGAGCTAATTT)
Components
  • (DNA (27-MER)) x 2
  • DNA-binding protein Fis
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / HTH domain / DNA bending / indirect recognition / 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 repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation / protein-DNA complex / nucleosome / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol
Similarity search - Function
DNA-binding protein Fis / : / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein Fis
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.561 Å
AuthorsHancock, S.P. / Cascio, D. / Johnson, R.C.
CitationJournal: Plos One / Year: 2016
Title: DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
Authors: Hancock, S.P. / Stella, S. / Cascio, D. / Johnson, R.C.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_prerelease_seq / 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
A: DNA-binding protein Fis
B: DNA-binding protein Fis
C: DNA (27-MER)
D: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)39,0914
Polymers39,0914
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-61 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.290, 93.950, 154.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (strain K12) (bacteria)
Strain: K12 / Gene: fis, b3261, JW3229 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6R3
#2: DNA chain DNA (27-MER)


Mass: 8334.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8250.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.56→154.51 Å / Num. obs: 19332 / % possible obs: 91.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 38.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Net I/σ(I): 14.7 / Num. measured all: 112418 / Scaling rejects: 107
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.56-2.73.70.692.2705819030.7850.39763.5
8.1-154.515.10.04529.836817150.9980.02192.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.14data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IV5

3iv5


Resolution: 2.561→45.162 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 937 4.93 %
Rwork0.2229 18083 -
obs0.2243 19020 90.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177 Å2 / Biso mean: 57.283 Å2 / Biso min: 15.71 Å2
Refinement stepCycle: final / Resolution: 2.561→45.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 4 2610
Biso mean---32.23 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172766
X-RAY DIFFRACTIONf_angle_d1.0433942
X-RAY DIFFRACTIONf_chiral_restr0.042450
X-RAY DIFFRACTIONf_plane_restr0.005320
X-RAY DIFFRACTIONf_dihedral_angle_d26.5761128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5609-2.69590.2922850.27371520160554
2.6959-2.86480.33071290.29228242953100
2.8648-3.08590.2971470.281828112958100
3.0859-3.39640.30541480.250428032951100
3.3964-3.88760.21191230.21242401252486
3.8876-4.89710.22041480.18082769291798
4.8971-45.16930.22551570.1962955311297
Refinement TLS params.Method: refined / Origin x: -11.2333 Å / Origin y: 2.0456 Å / Origin z: -5.5791 Å
111213212223313233
T0.3873 Å2-0.0642 Å2-0.0081 Å2-0.3692 Å20.0126 Å2--0.3108 Å2
L1.6502 °20.0185 °20.5555 °2-1.3064 °2-0.051 °2--2.4047 °2
S0.025 Å °0.1575 Å °-0.3787 Å °-0.2514 Å °0.2225 Å °0.0132 Å °0.9357 Å °-0.1394 Å °-0.1957 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 98
2X-RAY DIFFRACTION1allB1 - 98
3X-RAY DIFFRACTION1allC1 - 27
4X-RAY DIFFRACTION1allD1 - 27
5X-RAY DIFFRACTION1allE1 - 4

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