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- PDB-2h1o: Structure of FitAB bound to IR36 DNA fragment -

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Basic information

Entry
Database: PDB / ID: 2h1o
TitleStructure of FitAB bound to IR36 DNA fragment
Components
  • IR36-strand 1
  • IR36-strand 2
  • Trafficking protein A
  • Trafficking protein B
KeywordsGENE REGULATION/DNA COMPLEX / PIN domain / RHH protein / DNA binding / tetramer of dimers / GENE REGULATION-DNA COMPLEX COMPLEX
Function / homology
Function and homology information


migration in host / RNA nuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / DNA binding
Similarity search - Function
: / Antitoxin FitA-like, ribbon-helix-helix / : / PIN domain / VapC family / Met repressor-like / Arc Repressor Mutant / 5'-nuclease / Arc-type ribbon-helix-helix / Ribbon-helix-helix ...: / Antitoxin FitA-like, ribbon-helix-helix / : / PIN domain / VapC family / Met repressor-like / Arc Repressor Mutant / 5'-nuclease / Arc-type ribbon-helix-helix / Ribbon-helix-helix / PIN domain / PIN-like domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin FitA / Toxin FitB / Toxin FitB / Antitoxin FitA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.
Authors: Mattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: IR36-strand 1
V: IR36-strand 2
A: Trafficking protein B
B: Trafficking protein B
C: Trafficking protein B
D: Trafficking protein B
E: Trafficking protein A
F: Trafficking protein A
G: Trafficking protein A
H: Trafficking protein A


Theoretical massNumber of molelcules
Total (without water)115,17910
Polymers115,17910
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.040, 82.403, 135.503
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain IR36-strand 1


Mass: 11169.996 Da / Num. of mol.: 1 / Mutation: iodo / Source method: obtained synthetically / Details: sequence upstream of FitAB promoter region
#2: DNA chain IR36-strand 2


Mass: 11198.117 Da / Num. of mol.: 1 / Mutation: iodo / Source method: obtained synthetically / Details: sequence upstream of FitAB promoter region
#3: Protein
Trafficking protein B


Mass: 15919.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q9RF91, UniProt: Q5F882*PLUS
#4: Protein
Trafficking protein A


Mass: 7283.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q9RF92, UniProt: Q5F881*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium acetate, pH 4.0, 0.27 M sodium acetate, pH 7.0, 7.2 % PEG 20,000, 7.2 % PEG monomethyl ether 550, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2PEG11
3PEG monomethyl ether11
4H2O11
5sodium acetate12
6PEG12
7PEG monomethyl ether12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.99→70.36 Å / Num. all: 33360 / Num. obs: 33243 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Rsym value: 0.178 / Net I/σ(I): 3.1
Reflection shellResolution: 2.99→3.14 Å / Mean I/σ(I) obs: 44 / Rsym value: 0.015 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H1C

2h1c


Resolution: 3→70.36 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3316 10 %random
Rwork0.212 ---
all0.269 33257 --
obs0.269 33243 100 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 25.6821 Å2 / ksol: 0.316642 e/Å3
Displacement parametersBiso mean: 40.87 Å2
Baniso -1Baniso -2Baniso -3
1-17.49 Å20 Å2-12.4 Å2
2---17.57 Å20 Å2
3---0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→70.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 1470 0 46 7906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3-3.140.3933809.30.32737150.024100409599.9
3.14-3.30.32842810.40.25937040.0164137413299.9
3.3-3.510.30241210.10.24336790.0154096409199.9
3.51-3.780.2894089.70.21437790.0144191418799.9
3.78-4.160.27244210.60.19737110.01341544153100
4.16-4.760.233415100.18137280.0114145414399.9
4.76-60.273939.40.21237840.01441784177100
6-70.360.21343810.30.17638270.014276426599.7

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