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

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Basic information

Entry
Database: PDB / ID: 4ihw
TitleCrystal structure of Fis bound to 27 bp Inosine substituted DNA F28-dI (AAATTTGTTTGAICITTGAGCAAATTT)
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: 2.7 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)39,0494
Polymers39,0494
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-64 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.370, 94.400, 154.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 8330.388 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 27-bp DNA Strand B


Mass: 8212.348 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 4.06 Å3/Da / Density % sol: 69.72 %
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: Oct 17, 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: 2.7→100 Å / Num. obs: 17708 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 6.56 % / Biso Wilson estimate: 66.903 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-2.770.8482.85195.8
2.77-2.850.6943.49198.9
2.85-2.930.5344.41199.4
2.93-3.020.4275.48199.2
3.02-3.120.2547.48198.9
3.12-3.230.15810.44198.7
3.23-3.350.12912.89198.5
3.35-3.490.11714.82197.5
3.49-3.640.10316.64196.7
3.64-3.820.09118.78197.7
3.82-4.030.08519.7197.1
4.03-4.270.07122.11196.7
4.27-4.560.06623.01197.5
4.56-4.930.05823.33197
4.93-5.40.05724.43198.5
5.4-6.040.05625.7198.8
6.04-6.970.04926.1198.3
6.97-8.540.04426.88196.7
8.54-12.080.04126.11187.3
12.080.03523.98163.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å45.15 Å
Translation2.7 Å45.15 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: 2.7→45.32 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.99 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1768 10 %
Rwork0.2208 --
obs0.2247 17677 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.6722 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1098 0 0 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012755
X-RAY DIFFRACTIONf_angle_d1.5743936
X-RAY DIFFRACTIONf_dihedral_angle_d25.7521116
X-RAY DIFFRACTIONf_chiral_restr0.077450
X-RAY DIFFRACTIONf_plane_restr0.004320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.77310.38541300.31441175X-RAY DIFFRACTION96
2.7731-2.85470.34251360.30971219X-RAY DIFFRACTION99
2.8547-2.94680.34511360.29391221X-RAY DIFFRACTION99
2.9468-3.05210.33681380.30181236X-RAY DIFFRACTION99
3.0521-3.17430.33291340.28721206X-RAY DIFFRACTION99
3.1743-3.31870.33471350.27211224X-RAY DIFFRACTION98
3.3187-3.49360.2971360.23821220X-RAY DIFFRACTION97
3.4936-3.71240.30681340.23461210X-RAY DIFFRACTION97
3.7124-3.99890.23941360.23091221X-RAY DIFFRACTION97
3.9989-4.4010.2431370.20011229X-RAY DIFFRACTION97
4.401-5.03710.22081370.18391239X-RAY DIFFRACTION97
5.0371-6.34340.22181420.18821273X-RAY DIFFRACTION98
6.3434-45.32650.20051370.1751236X-RAY DIFFRACTION89

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