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- PDB-3jrb: Crystal structure of Fis bound to 27 bp DNA F24 containing T-trac... -

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Basic information

Entry
Database: PDB / ID: 3jrb
TitleCrystal structure of Fis bound to 27 bp DNA F24 containing T-tract at center
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: 3.1 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
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-66 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.573, 94.264, 155.336
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: 8316.388 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8268.428 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.08 Å3/Da / Density % sol: 69.86 %
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: 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: 11692 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.141 / Χ2: 1.842 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.214.60.62611300.734199
3.21-3.344.70.48111560.788199.1
3.34-3.494.60.46111292.325199
3.49-3.684.70.38311562.401199
3.68-3.914.70.32711423.442199.5
3.91-4.214.70.19611511.713199.2
4.21-4.634.70.14511651.776199.7
4.63-5.34.60.13111871.671199.7
5.3-6.684.40.11112021.558199.6
6.68-904.30.07712742.011197.8

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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: 3.1→80.58 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.578 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 557 4.8 %RANDOM
Rwork0.239 ---
obs0.242 11659 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.54 Å2 / Biso mean: 75.589 Å2 / Biso min: 11.23 Å2
Refinement stepCycle: LAST / Resolution: 3.1→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 15 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.473942
X-RAY DIFFRACTIONr_angle_other_deg1.10933785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75625.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.99915303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4621511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.070.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.2340.2717
X-RAY DIFFRACTIONr_nbd_other0.2070.21682
X-RAY DIFFRACTIONr_nbtor_refined0.2150.21210
X-RAY DIFFRACTIONr_nbtor_other0.0880.21164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4490.23
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)2.96121213
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.4442382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)3.831511
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)1.53222355
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)2.43532431
LS refinement shellResolution: 3.097→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 17 -
Rwork0.346 351 -
all-368 -
obs--42.2 %
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)
10.9465-0.3757-0.00343.18460.5642.9756-0.12450.01420.01960.43570.2140.01090.42940.1786-0.0896-0.13170.0241-0.00240.044-0.0033-0.065112.924310.74678.9473
21.23690.0573-0.81782.21730.06563.01870.0231-0.149-0.05130.06030.06440.07360.30680.0646-0.0874-0.19470.0379-0.01880.0422-0.00870.01129.899811.2752.2237
30.90.03670.98560.52780.23446.11120.2103-0.0092-0.63910.2090.24470.07071.46340.2097-0.4550.28060.0893-0.0324-0.20780.0259-0.114411.7246-10.11955.3291
40.69030.46181.29250.90541.27237.60890.2376-0.0644-0.5420.32150.09240.04191.3406-0.1162-0.330.21260.0314-0.0517-0.2722-0.0274-0.133410.7116-10.10696.0941
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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