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- PDB-3jrd: Crystal structure of Fis bound to 27 bp DNA F25 containing T2A3 s... -

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Basic information

Entry
Database: PDB / ID: 3jrd
TitleCrystal structure of Fis bound to 27 bp DNA F25 containing T2A3 sequence 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 regulatio / 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: 3.1 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 area8750 Å2
ΔGint-63 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.296, 93.076, 155.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asymmetric unit

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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: 8343.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8241.386 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 Å3/Da / Density % sol: 69.23 %
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, 38% 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: 3.1→90 Å / Num. obs: 10882 / % possible obs: 91 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.186 / Χ2: 1.795 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.2140.66610681.426193.8
3.21-3.343.90.45210902.179191.8
3.34-3.4940.35510551.883192.7
3.49-3.6840.28511011.377192.4
3.68-3.9140.21810852.304190.9
3.91-4.2140.17710671.57191.7
4.21-4.6340.13510842.193190.9
4.63-5.340.13510831.659189.5
5.3-6.683.90.1311031.413190
6.68-903.70.15211461.949186.6

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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: 3.1→79.81 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.304 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 512 4.7 %RANDOM
Rwork0.242 ---
obs0.245 10795 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.57 Å2 / Biso mean: 82.247 Å2 / Biso min: 49.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 0 2606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0020.021523
X-RAY DIFFRACTIONr_angle_refined_deg2.0942.473942
X-RAY DIFFRACTIONr_angle_other_deg1.13633785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.75125.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3781511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0820.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.2140.2588
X-RAY DIFFRACTIONr_nbd_other0.2060.21633
X-RAY DIFFRACTIONr_nbtor_refined0.2170.21195
X-RAY DIFFRACTIONr_nbtor_other0.0950.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.26
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)3.46221199
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.592382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)4.39531511
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)2.2122356
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)3.26332431
LS refinement shellResolution: 3.097→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 26 -
Rwork0.306 679 -
all-705 -
obs--84.63 %
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)
12.2834-0.73151.29775.4117-0.93113.9208-0.27020.02560.2230.37150.3239-0.1315-0.27790.211-0.0537-0.3623-0.0081-0.0052-0.1968-0.0672-0.174912.795210.60828.9085
22.46390.1422-0.4375.37960.11584.1243-0.3783-0.18450.226-0.09860.34320.0957-0.11790.14050.0351-0.3540.0704-0.0332-0.22860.0344-0.17819.868911.00552.1874
31.81170.07523.53850.98460.304113.79170.63390.1171-0.79460.08420.30920.0962.46880.3539-0.9431-0.04210.057-0.0821-0.48850.027-0.162111.612-10.29655.3213
41.81920.10622.34011.1903-0.113111.70060.43790.0804-0.67470.04060.3183-0.00432.1594-0.1732-0.75610.0027-0.0074-0.0936-0.56-0.0446-0.216810.6778-10.24666.0949
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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