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- PDB-4ihy: Crystal structure of Fis bound to 27bp Inosine substituted DNA F2... -

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Basic information

Entry
Database: PDB / ID: 4ihy
TitleCrystal structure of Fis bound to 27bp Inosine substituted DNA F29-dI (AAATTTGTTTGIICICTGAGCAAATTT)
Components
  • 27-bp DNA Strand A
  • 27-bp DNA Strand B
  • DNA-binding protein fis
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / HTH domain / minor groove compression / DNA bending / indirect recognition / TRANSCRIPTION-DNA complex
Function / homologyHomeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / DNA / DNA (> 10) / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsHancock, S.P. / Cascio, D. / Johnson, R.C.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
Authors: Hancock, S.P. / Ghane, T. / Cascio, D. / Rohs, R. / Di Felice, R. / Johnson, R.C.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Sep 20, 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: 27-bp DNA Strand A
D: 27-bp DNA Strand B


Theoretical massNumber of molelcules
Total (without water)39,0214
Polymers39,0214
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-63 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 94.050, 155.040
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


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ECDH1ME8569_3147, EcDH1_0445, fis / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QXL3
#2: DNA chain 27-bp DNA Strand A


Mass: 8316.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 27-bp DNA Strand B


Mass: 8198.321 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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: 4.04 Å3/Da / Density % sol: 69.53 %
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% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Jul 24, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 14611 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.72 % / Biso Wilson estimate: 69.195 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-2.980.9472.197852104899.9
2.98-3.060.7662.738578104399.8
3.06-3.150.4954.02802699699.7
3.15-3.240.3235.417909983100
3.24-3.350.2716.16780396499.8
3.35-3.470.2137.46708389699.7
3.47-3.60.1828.71718890299.1
3.6-3.740.1649.81662984899.8
3.74-3.910.13910.78655583199.9
3.91-4.10.12512.56597578399.1
4.1-4.320.10614.38582576199.2
4.32-4.590.09515.25527769499.1
4.59-4.90.08915.65525968498.8
4.9-5.290.09115.31469462799.7
5.29-5.80.08716.24432058499.8
5.8-6.480.08416.353851544100
6.48-7.490.07183532483100
7.49-9.170.06619.07297141199.8
9.17-12.970.0619.41230233799.7
12.970.06318.06113919295

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.54 Å77.52 Å
Translation7.54 Å77.52 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IV5

3iv5


Resolution: 2.9→59.819 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7023 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 34.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2704 1451 9.97 %RANDOM
Rwork0.2279 ---
obs0.2323 14553 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.63 Å2 / Biso mean: 38.8703 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: LAST / Resolution: 2.9→59.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1096 0 4 2605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092757
X-RAY DIFFRACTIONf_angle_d1.5573932
X-RAY DIFFRACTIONf_chiral_restr0.076450
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d26.3091108
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 (%)
2.9-3.00370.41841400.324412581398100
3.0037-3.1240.34971450.307113111456100
3.124-3.26610.3111410.28711274141599
3.2661-3.43830.35731430.25521283142699
3.4383-3.65370.29181440.24481302144699
3.6537-3.93580.28691450.231613181463100
3.9358-4.33170.24721440.21931300144499
4.3317-4.95830.23981450.20361300144599
4.9583-6.24590.25621480.223713471495100
6.2459-59.83180.22591560.19021409156598

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