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- PDB-3jri: Crystal structure of Fis bound to 27 bp non consensus sequence DNA F23 -

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Basic information

Entry
Database: PDB / ID: 3jri
TitleCrystal structure of Fis bound to 27 bp non consensus sequence DNA F23
Components
  • (DNA (27-MER)) x 2
  • DNA-binding protein fis
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / HTH domain / minor groove compression / DNA bending / indirect recognition / activator / DNA-binding / Transcription / Transcription regulation / 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 repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / response to radiation / protein-DNA complex / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsStella, S. / Cascio, D. / Johnson, R.C.
CitationJournal: Genes Dev. / Year: 2010
Title: The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.
Authors: Stella, S. / Cascio, D. / Johnson, R.C.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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: DNA (27-MER)
D: DNA (27-MER)


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 area8680 Å2
ΔGint-57 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.222, 92.635, 154.863
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


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: 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: 8334.415 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8250.399 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: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→90 Å / Num. obs: 11811 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.144 / Χ2: 1.812 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.215.10.60511081.75197.6
3.21-3.345.90.47611581.607199.5
3.34-3.496.60.44311341.5131100
3.49-3.686.80.30911711.5661100
3.68-3.916.90.24711821.651100
3.91-4.216.80.17611701.4841100
4.21-4.636.80.12811821.5451100
4.63-5.36.70.12911881.5981100
5.3-6.686.50.1112092.0171100
6.68-906.10.0913093.354199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IV5

3iv5


Resolution: 3.11→79.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.334 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 559 4.8 %RANDOM
Rwork0.23 ---
obs0.232 11756 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.14 Å2 / Biso mean: 85.056 Å2 / Biso min: 72.38 Å2
Refinement stepCycle: LAST / Resolution: 3.11→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 0 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0050.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.8422.473942
X-RAY DIFFRACTIONr_angle_other_deg1.09633785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.14125.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7771511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0720.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.2270.2664
X-RAY DIFFRACTIONr_nbd_other0.2060.21705
X-RAY DIFFRACTIONr_nbtor_refined0.2170.21244
X-RAY DIFFRACTIONr_nbtor_other0.0930.21184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.24
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)0.7321.51200
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.1091.5382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)0.87121511
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)1.27132350
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)1.9184.52431
LS refinement shellResolution: 3.107→3.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 39 -
Rwork0.323 759 -
all-798 -
obs--95.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97611.16550.14136.23120.31615.9415-0.18610.08940.0113-0.69350.17820.16740.8033-0.30040.0079-0.46150.0480.0302-0.25580.0557-0.4341-12.754110.499-9.0094
23.4822-1.7275-0.65885.0038-0.47453.7720.00350.2420.1178-0.21210.038-0.22070.3485-0.0173-0.0415-0.4648-0.0913-0.0211-0.4018-0.0412-0.4432-9.709810.9117-2.1734
31.9456-0.16723.44651.3677-0.956511.37290.74210.0944-0.815-0.20580.2845-0.00012.2087-0.164-1.02660.2228-0.0262-0.0624-0.2978-0.0297-0.1768-11.4663-10.2893-5.4897
42.0740.08053.76730.2857-0.418215.23720.65-0.0106-0.6377-0.23870.2312-0.03262.0517-0.2578-0.88110.3672-0.0075-0.1114-0.45570.0213-0.1416-10.5476-10.2952-6.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 98
2X-RAY DIFFRACTION2B1 - 98
3X-RAY DIFFRACTION3C1 - 27
4X-RAY DIFFRACTION4D1 - 27

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