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- PDB-4lsy: Crystal structure of copper-bound L66S mutant toxin from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 4lsy
TitleCrystal structure of copper-bound L66S mutant toxin from Helicobacter pylori
ComponentsUncharacterized protein, Toxin
KeywordsTOXIN / Toxin-antitoxin / Copper bound
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
COPPER (II) ION / CITRATE ANION / Addiction module toxin RelE
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein, Toxin
B: Uncharacterized protein, Toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5544
Polymers21,3012
Non-polymers2532
Water3,657203
1
A: Uncharacterized protein, Toxin


Theoretical massNumber of molelcules
Total (without water)10,6501
Polymers10,6501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein, Toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9033
Polymers10,6501
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.740, 83.998, 41.499
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein, Toxin


Mass: 10650.441 Da / Num. of mol.: 2 / Mutation: L66S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: C694_04590, HP_0894 / Plasmid: pET15b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: O25554
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
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: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 18, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 13555

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LS4

4ls4


Resolution: 1.895→29.042 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8254 / SU ML: 0.22 / σ(F): 0 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 653 4.9 %
Rwork0.1989 --
obs0.2019 13318 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.308 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 58.38 Å2 / Biso mean: 22.7698 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.1763 Å20 Å22.303 Å2
2--1.7595 Å20 Å2
3---1.4169 Å2
Refinement stepCycle: LAST / Resolution: 1.895→29.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 14 203 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071499
X-RAY DIFFRACTIONf_angle_d1.1042012
X-RAY DIFFRACTIONf_dihedral_angle_d15.447593
X-RAY DIFFRACTIONf_chiral_restr0.072224
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8954-2.04180.32391260.2207255895
2.0418-2.24720.27781510.2047253996
2.2472-2.57220.2641280.2084259997
2.5722-3.240.29081390.20622684100
3.24-29.04550.2121090.1816228584

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