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- PDB-4ltt: Crystal structure of native apo toxin from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4ltt
TitleCrystal structure of native apo toxin from Helicobacter pylori
ComponentsUncharacterized protein, toxin
KeywordsTOXIN / Toxin-antitoxin
Function / homology
Function and homology information


mRNA catabolic process / translational termination / RNA endonuclease activity / metal ion binding
Similarity search - Function
Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Addiction module toxin RelE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsLee, B.J. / Im, H. / Pathak, C.C. / Yoon, H.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure of apo and copper bound HP0894 toxin from Helicobacter pylori 26695 and insight into mRNase activity
Authors: Pathak, C. / Im, H. / Yang, Y.J. / Yoon, H.J. / Kim, H.M. / Kwon, A.R. / Lee, B.J.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein, toxin


Theoretical massNumber of molelcules
Total (without water)10,8681
Polymers10,8681
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.656, 36.589, 87.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein, toxin


Mass: 10867.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: C694_04590, HP_0894 / Production host: Escherichia coli (E. coli) / References: UniProt: O25554
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. obs: 21963

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LS4

4ls4


Resolution: 1.28→28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.754 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21164 1125 5.1 %RANDOM
Rwork0.17968 ---
obs0.18124 20784 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2---0.11 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.28→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 0 190 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02788
X-RAY DIFFRACTIONr_angle_refined_deg2.1652.0071060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.082594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56125.27836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.664153
X-RAY DIFFRACTIONr_chiral_restr0.1470.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021573
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 83 -
Rwork0.188 1326 -
obs--93.44 %

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