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- PDB-5e3n: Crystal structure of Fis bound to 27bp DNA F31 (AAATTTGTAGGAATTTT... -

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Basic information

Entry
Database: PDB / ID: 5e3n
TitleCrystal structure of Fis bound to 27bp DNA F31 (AAATTTGTAGGAATTTTCTGCAAATTT)
Components
  • (DNA (27-MER)) x 2
  • DNA-binding protein Fis
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / HTH domain / DNA bending / indirect recognition / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsHancock, S.P. / Cascio, D. / Johnson, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM038509 United States
CitationJournal: Plos One / Year: 2016
Title: DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
Authors: Hancock, S.P. / Stella, S. / Cascio, D. / Johnson, R.C.
History
DepositionOct 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation

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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
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-60 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.190, 92.980, 153.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA8 - 98
211chain BB1 - 98
112chain CC1 - 27
212chain DD1 - 27

NCS ensembles :
ID
1
2

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Components

#1: Protein DNA-binding protein Fis / Factor-for-inversion stimulation protein / Hin recombinational enhancer-binding protein


Mass: 11252.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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: 8319.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8266.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.95 Å3/Da / Density % sol: 68.89 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.66→92.98 Å / Num. obs: 18640 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 29.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.038 / Net I/σ(I): 10.3 / Num. measured all: 142367 / Scaling rejects: 267
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.66-2.87.30.622.51935726640.9180.24199.9
8.4-92.986.50.06117.643596750.9940.02698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
PHASER2.2.1phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→39.794 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 892 5.05 %
Rwork0.2166 16766 -
obs0.2184 17658 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.28 Å2 / Biso mean: 38.7081 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 2.66→39.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 1101 0 9 2615
Biso mean---19.09 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142766
X-RAY DIFFRACTIONf_angle_d1.1313942
X-RAY DIFFRACTIONf_chiral_restr0.044450
X-RAY DIFFRACTIONf_plane_restr0.005320
X-RAY DIFFRACTIONf_dihedral_angle_d24.3221128
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1096X-RAY DIFFRACTION9.976TORSIONAL
12B1096X-RAY DIFFRACTION9.976TORSIONAL
21C442X-RAY DIFFRACTION9.976TORSIONAL
22D442X-RAY DIFFRACTION9.976TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.659-2.82560.3131100.28432014212470
2.8256-3.04370.32461610.274828853046100
3.0437-3.34980.28321480.250829123060100
3.3498-3.83420.22391430.212729253068100
3.8342-4.82930.22731670.18329493116100
4.8293-39.79890.2231630.18253081324499
Refinement TLS params.Method: refined / Origin x: -11.061 Å / Origin y: 1.7376 Å / Origin z: -5.5781 Å
111213212223313233
T0.2283 Å2-0.0234 Å2-0.0377 Å2-0.1984 Å20.0158 Å2--0.0935 Å2
L1.1684 °20.0429 °20.367 °2-0.6308 °2-0.0575 °2--1.6921 °2
S0.0497 Å °0.0758 Å °-0.2209 Å °-0.0926 Å °0.0963 Å °-0.0053 Å °0.6558 Å °-0.0591 Å °-0.0902 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 98
2X-RAY DIFFRACTION1allB1 - 98
3X-RAY DIFFRACTION1allB99 - 103
4X-RAY DIFFRACTION1allC1 - 27
5X-RAY DIFFRACTION1allC28
6X-RAY DIFFRACTION1allD1 - 27
7X-RAY DIFFRACTION1allE1 - 4

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