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- PDB-4ihv: Crystal structure of Fis bound to 27 bp sequence DNA F28 (AAATTTG... -

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Basic information

Entry
Database: PDB / ID: 4ihv
TitleCrystal structure of Fis bound to 27 bp sequence DNA F28 (AAATTTGTTTGAGCGTTGAGCAAATTT)
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: 2.716 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)39,0944
Polymers39,0944
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-65 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.790, 89.390, 154.150
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: 8360.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 27-bp DNA Strand B


Mass: 8227.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.77 Å3/Da / Density % sol: 67.38 %
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: 0.92017 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: 0.92017 Å / Relative weight: 1
ReflectionResolution: 2.716→100 Å / Num. obs: 16603 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.99 % / Biso Wilson estimate: 63.279 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.716-2.790.882.388028117397.5
2.79-2.860.7093.0287731194100
2.86-2.950.5573.9482211117100
2.95-3.040.4225.181861125100
3.04-3.140.2877.117769106799.8
3.14-3.250.18110.4376331057100
3.25-3.370.14612.24714699599.9
3.37-3.510.10915.67703098499.9
3.51-3.660.09717.66743948100
3.66-3.840.08120.05632889599.9
3.84-4.050.0722.93597685699.8
4.05-4.290.06125.5575683799.6
4.29-4.590.05427.515157754100
4.59-4.960.05227.39494472799.9
4.96-5.430.05228.1436565999.7
5.43-6.070.05327.97399761699.5
6.07-7.010.04630.05350753999.8
7.01-8.590.03733.64308847499.8
8.59-12.150.03334.91226536799.2
12.150.03431.91118621994

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.43 Å77.08 Å
Translation7.43 Å77.08 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IV5

3iv5


Resolution: 2.716→42.927 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7835 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1659 10.01 %RANDOM
Rwork0.2169 ---
obs0.221 16577 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.7 Å2 / Biso mean: 38.3474 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: LAST / Resolution: 2.716→42.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 5 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082752
X-RAY DIFFRACTIONf_angle_d1.4913942
X-RAY DIFFRACTIONf_chiral_restr0.075450
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d26.3361128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.716-2.7960.3491320.29861182131498
2.796-2.88620.34141370.27712321369100
2.8862-2.98930.3011350.263112161351100
2.9893-3.1090.30371360.258812291365100
3.109-3.25040.271360.230512171353100
3.2504-3.42170.26221370.226112411378100
3.4217-3.6360.24971380.208212431381100
3.636-3.91660.26441390.220812511390100
3.9166-4.31040.27771380.208512411379100
4.3104-4.93340.2511400.196212531393100
4.9334-6.21250.25231420.205612781420100
6.2125-42.93240.19821490.19821335148498

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