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- PDB-2bsq: FitAB bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2bsq
TitleFitAB bound to DNA
Components
  • IR36, FORWARD STRAND
  • IR36, REVERSE STRAND
  • TRAFFICKING PROTEIN A
  • TRAFFICKING PROTEIN B
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION COMPLEX / PIN DOMAIN / RIBBON-HELIX-HELIX / DNA BINDING / HETERODIMER
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
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 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
I: IR36, FORWARD STRAND
J: IR36, REVERSE STRAND


Theoretical massNumber of molelcules
Total (without water)120,95710
Polymers120,95710
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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: Protein
TRAFFICKING PROTEIN B / FITB


Mass: 16333.761 Da / Num. of mol.: 4 / Fragment: PIN DOMAIN, RESIDUES 1-139 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5F882
#2: Protein
TRAFFICKING PROTEIN A / FITA


Mass: 8313.364 Da / Num. of mol.: 4 / Fragment: DNA-BINDING PROTEIN, RESIDUES 2-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5F881
#3: DNA chain IR36, FORWARD STRAND


Mass: 11169.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA GONORRHOEAE (bacteria)
#4: DNA chain IR36, REVERSE STRAND


Mass: 11198.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA GONORRHOEAE (bacteria)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 139 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 139 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, ASP 139 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 139 TO LEU ENGINEERED RESIDUE IN CHAIN C, ASP 139 TO LEU ENGINEERED RESIDUE IN CHAIN D, ASP 139 TO LEU

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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: 3.45 Å3/Da / Density % sol: 67.38 %
Description: MODEL FILE NOT YET RELEASED-WILL BE IN SAME PAPER
Crystal growpH: 4.5
Details: 0.1 M ACETATE, PH 4.0 7.2 % PEG 20,000 7.2 % PEG 550 MME 0.26 M NA ACETATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332
DetectorType: ADSC CCD / 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: 3→81.65 Å / Num. obs: 16708 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH4

1yh4
PDB Unreleased entry


Resolution: 3→70.36 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1657362.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3316 10 %RANDOM
Rwork0.213 ---
obs0.213 33243 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4919 Å2 / ksol: 0.315881 e/Å3
Displacement parametersBiso mean: 40.7 Å2
Baniso -1Baniso -2Baniso -3
1-17.45 Å20 Å2-12.41 Å2
2---17.53 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→70.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 1470 0 45 7910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.362.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 518 9.5 %
Rwork0.309 4959 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP

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