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- PDB-4ihx: Crystal structure of Fis bound to 27 bp 2-Aminopurine substituted... -

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Basic information

Entry
Database: PDB / ID: 4ihx
TitleCrystal structure of Fis bound to 27 bp 2-Aminopurine substituted DNA F28-2AP (AAATTTGTTTGA2T2TTGAGCAAATTT)
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: 2.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)39,0914
Polymers39,0914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-54 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.120, 91.590, 154.020
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: 8343.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 27-bp DNA Strand B


Mass: 8241.385 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: 3.89 Å3/Da / Density % sol: 68.38 %
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: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 15566 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.81 % / Biso Wilson estimate: 78.611 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.870.9542.0367981137100
2.87-2.950.6622.976556109399.8
2.95-3.040.4773.866256107698.9
3.04-3.130.3225.045486101497.6
3.13-3.230.2237.696023100398.5
3.23-3.350.1649.86226101199.9
3.35-3.470.12112.45560093299.9
3.47-3.610.10114.37566094799.9
3.61-3.780.08217.26508485699.8
3.78-3.960.06719.59488484898.9
3.96-4.170.05622.46418778396.5
4.17-4.430.04827.51468776799.1
4.43-4.730.04528.68430871499
4.73-5.110.04628.07398568099.7
5.11-5.60.04528.84352963199.8
5.6-6.260.04327.93290055595.7
6.26-7.230.03633.03300652099.6
7.23-8.850.03236.86240643198.9
8.85-12.520.0337.3171035098.9
12.520.0340.57109521899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å78.72 Å
Translation2.8 Å78.72 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: 2.8→78.723 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7517 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1556 10.02 %RANDOM
Rwork0.2162 ---
obs0.2204 15528 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.06 Å2 / Biso mean: 41.0496 Å2 / Biso min: 7.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→78.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 0 2606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012755
X-RAY DIFFRACTIONf_angle_d1.4833942
X-RAY DIFFRACTIONf_chiral_restr0.072450
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d27.611116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.89030.34581420.315712741416100
2.8903-2.99360.36631350.29711214134999
2.9936-3.11350.32171390.2791248138798
3.1135-3.25520.31051360.25551232136898
3.2552-3.42680.27551410.228112601401100
3.4268-3.64150.28781410.225512661407100
3.6415-3.92260.28121430.21691295143899
3.9226-4.31740.24251390.2081241138097
4.3174-4.9420.23841400.18811265140599
4.942-6.2260.24391450.21991300144598
6.226-78.75360.22311550.18911377153298

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