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- PDB-3jre: Crystal structure of Fis bound to 27 bp DNA F26 containing A-trac... -

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Basic information

Entry
Database: PDB / ID: 3jre
TitleCrystal structure of Fis bound to 27 bp DNA F26 containing A-tract 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 / protein-DNA complex ...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 / protein-DNA complex / response to radiation / 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: 3.17 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)39,0914
Polymers39,0914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-64 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.638, 94.215, 155.272
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: 8361.458 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8223.357 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: 4.08 Å3/Da / Density % sol: 69.87 %
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% 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 / Date: Feb 25, 2008
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→90 Å / Num. obs: 9497 / % possible obs: 83.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.196 / Χ2: 1.714 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.15-3.265.70.7179502.199186.1
3.26-3.395.60.5229531.964187.2
3.39-3.555.70.4549552.212185.3
3.55-3.735.60.4139452.515186.4
3.73-3.975.70.3429502.607184.7
3.97-4.285.70.1929381.338183.6
4.28-4.715.70.1599391.237183.9
4.71-5.395.70.1439471.111182.6
5.39-6.795.50.1189360.852182.2
6.79-905.40.1069841.056178.2

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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: 3.17→80.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 440 4.7 %RANDOM
Rwork0.209 ---
obs0.21 9418 82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.11 Å2 / Biso mean: 69.334 Å2 / Biso min: 37.71 Å2
Refinement stepCycle: LAST / Resolution: 3.17→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 0 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg2.0612.473942
X-RAY DIFFRACTIONr_angle_other_deg1.11433785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.825.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49715303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0770.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.1980.2520
X-RAY DIFFRACTIONr_nbd_other0.2030.21496
X-RAY DIFFRACTIONr_nbtor_refined0.210.21168
X-RAY DIFFRACTIONr_nbtor_other0.0960.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.24
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)3.32721219
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.5072382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)4.16731511
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)1.98222369
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)3.07632431
LS refinement shellResolution: 3.168→3.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 28 -
Rwork0.27 502 -
all-530 -
obs--63.86 %
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)
10.4268-0.13250.571.35530.44911.0596-0.16020.01840.11190.270.1923-0.08660.0119-0.0346-0.0322-0.06190.03480.0204-0.0106-0.0013-0.083612.955210.47428.9966
20.5483-0.03030.05030.7961-0.68621.0915-0.106-0.08370.1361-0.03320.14370.10350.009-0.0141-0.0377-0.0698-0.01240.0294-0.0415-0.0463-0.03779.977910.95272.2129
30.928-0.14651.31650.8733-0.56375.77520.34010.1999-0.41470.07790.33320.12160.66760.3606-0.67330.06980.0473-0.1245-0.3047-0.0421-0.130911.6032-10.77225.4462
41.0620.16421.64670.20920.40636.57840.2218-0.042-0.3395-0.01340.20840.09870.4663-0.3563-0.43020.0973-0.047-0.1217-0.3572-0.0121-0.179610.6835-10.72696.0677
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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