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- PDB-3jrf: Crystal structure of Fis bound to 27 bp DNA F27 containing a C/G ... -

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Basic information

Entry
Database: PDB / ID: 3jrf
TitleCrystal structure of Fis bound to 27 bp DNA F27 containing a C/G at center
Components
  • (DNA (27-MER)) x 2
  • DNA-binding protein fis
KeywordsDNA BINDING PROTEIN/DNA / HTH domain / Protein-DNA complex / 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 / 3IV5 / Resolution: 3.05 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 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)39,0924
Polymers39,0924
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8856 Å2
ΔGint-62 kcal/mol
Surface area19308 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.081, 92.173, 154.726
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


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: 8319.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8266.398 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 0.2 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: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→90 Å / Num. obs: 12039 / % possible obs: 99.7 %
Reflection shellResolution: 3.05→3.21 Å / Rmerge(I) obs: 0.599 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: 3IV5 / Resolution: 3.05→79.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.252 580 4.8 %
Rwork0.221 --
obs0.223 11995 97.3 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 75.38 Å2
Refinement stepCycle: LAST / Resolution: 3.05→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 6 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.8962.473942
X-RAY DIFFRACTIONr_angle_other_deg1.18233785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11125.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8621511
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.220.2573
X-RAY DIFFRACTIONr_nbd_other0.2160.21639
X-RAY DIFFRACTIONr_nbtor_refined0.2210.21188
X-RAY DIFFRACTIONr_nbtor_other0.0930.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.13 Å
RfactorNum. reflection% reflection
Rfree0.442 32 -
Rwork0.323 537 -
obs--65.86 %
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)
10.6758-0.20890.35211.93020.40141.6435-0.1022-0.02230.03610.3170.20660.01210.32140.0289-0.1045-0.10450.04560.0039-0.0991-0.01980.026812.727210.31868.9461
21.94770.7361-0.01272.1042-0.72771.9012-0.1548-0.17330.0373-0.0820.2201-0.00340.30130.1566-0.0653-0.20280.0538-0.0049-0.1196-0.03960.02449.819910.74882.2014
31.3977-0.02812.23020.55180.77188.02840.48560.0831-0.60210.12330.28890.09381.17010.5122-0.77450.11990.0912-0.1018-0.4338-0.00510.018811.5551-10.53455.3651
41.6910.27462.56370.33610.67979.22780.424-0.031-0.56210.16280.25660.01571.0981-0.2263-0.68060.1122-0.0098-0.1158-0.5211-0.0211-0.00610.5762-10.49616.1044
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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