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- PDB-5e3o: Crystal structure of Fis bound to 27bp DNA F32 (AAATTTGGAGGAATTTT... -

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Basic information

Entry
Database: PDB / ID: 5e3o
TitleCrystal structure of Fis bound to 27bp DNA F32 (AAATTTGGAGGAATTTTCTCCAAATTT)
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 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 / 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: 2.78 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
DepositionOct 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)39,0934
Polymers39,0934
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-66 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.190, 94.320, 154.340
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 (E. coli) / 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: 8304.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8282.396 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.: 8 / 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: 69.41 %
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: Mar 5, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.78→80.48 Å / Num. obs: 15712 / % possible obs: 94.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 39.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Net I/σ(I): 13.8 / Num. measured all: 80167 / Scaling rejects: 14
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
2.78-2.935.30.7192.61261623720.8620.34999.9
8.78-80.484.30.0362825085800.9990.01897

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
PHASER2.5.7phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→59.727 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 711 4.93 %
Rwork0.2199 13709 -
obs0.2222 14420 86.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.34 Å2 / Biso mean: 43.9852 Å2 / Biso min: 9.41 Å2
Refinement stepCycle: final / Resolution: 2.78→59.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 8 2614
Biso mean---23.44 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052759
X-RAY DIFFRACTIONf_angle_d0.8043942
X-RAY DIFFRACTIONf_chiral_restr0.031450
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d24.4171128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7777-2.99220.354930.31811921201462
2.9922-3.29320.32961600.27543104326499
3.2932-3.76970.28281230.22342457258079
3.7697-4.74910.22671610.19112977313894
4.7491-59.74030.23831740.18873250342498
Refinement TLS params.Method: refined / Origin x: -11.0468 Å / Origin y: 1.9724 Å / Origin z: -5.5341 Å
111213212223313233
T0.4 Å2-0.0305 Å2-0.0105 Å2-0.2474 Å20.019 Å2--0.0755 Å2
L1.5323 °20.0846 °20.5633 °2-0.8299 °20.0932 °2--2.2874 °2
S0.0887 Å °0.1247 Å °-0.3094 Å °-0.1823 Å °0.135 Å °0.0176 Å °0.7903 Å °-0.1014 Å °-0.087 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 - 10

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