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- PDB-3jrc: Crystal structure of Fis bound to 27 bp DNA F29 containing 5 G/Cs... -

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Basic information

Entry
Database: PDB / ID: 3jrc
TitleCrystal structure of Fis bound to 27 bp DNA F29 containing 5 G/Cs 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: 3.08 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)39,0964
Polymers39,0964
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-64 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.480, 93.640, 155.630
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: 8361.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8228.350 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.25 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 40% 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: Jan 1, 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: 11654 / % possible obs: 93.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.144 / Χ2: 1.565 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.214.50.6267351.242161.2
3.21-3.345.40.4359651.414178.5
3.34-3.496.30.41811241.477192.1
3.49-3.687.90.41712141.305198
3.68-3.918.80.33412221.355199.8
3.91-4.219.10.25412241.4521100
4.21-4.638.90.17512521.591100
4.63-5.38.30.14912611.5661100
5.3-6.687.80.14112751.723199.9
6.68-9010.30.09413822.01199.4

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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: 3.08→80.32 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.367 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 488 4.7 %RANDOM
Rwork0.23 ---
obs0.232 10306 83.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.92 Å2 / Biso mean: 63.353 Å2 / Biso min: 53.67 Å2
Refinement stepCycle: LAST / Resolution: 3.08→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 1101 0 2 2604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222748
X-RAY DIFFRACTIONr_bond_other_d0.0090.021520
X-RAY DIFFRACTIONr_angle_refined_deg1.2152.4713936
X-RAY DIFFRACTIONr_angle_other_deg0.97133777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2525187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02825.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03715301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2131511
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0520.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
X-RAY DIFFRACTIONr_nbd_refined0.1910.2610
X-RAY DIFFRACTIONr_nbd_other0.1990.21697
X-RAY DIFFRACTIONr_nbtor_refined0.20.21222
X-RAY DIFFRACTIONr_nbtor_other0.0810.21090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.25
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)0.3551.51232
X-RAY DIFFRACTIONMAIN-CHAIN BOND OTHER ATOMS (A''2)0.0241.5382
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)0.24921506
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)0.51432383
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)0.6274.52430
LS refinement shellResolution: 3.081→3.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 3 -
Rwork0.332 78 -
all-81 -
obs--9.18 %
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)
11.5643-1.18980.04055.34920.48754.6093-0.1496-0.2332-0.01890.45280.1813-0.22020.70150.1092-0.0317-0.158-0.02570.01210.0525-0.0283-0.238112.99810.64338.7646
23.33010.75350.07055.61220.02184.0911-0.0016-0.2988-0.00250.12350.01150.03340.347-0.0473-0.0099-0.258-0.00940.0233-0.0139-0.0106-0.23569.889511.09452.0211
31.34430.17682.92870.7590.76787.47390.77-0.0846-0.87040.27190.38570.06441.8980.4254-1.15570.65020.0463-0.07980.29390.06380.100411.681-10.19145.135
41.12170.21082.55520.42270.863610.64810.6152-0.0848-0.84490.22570.387-0.01491.93840.074-1.00230.66230.0394-0.12180.1858-0.05280.069410.7747-10.15875.6939
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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