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- PDB-4xgq: Crystal structure of addiction module from Mycobacterial species -

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Basic information

Entry
Database: PDB / ID: 4xgq
TitleCrystal structure of addiction module from Mycobacterial species
Components
  • Antitoxin VapB30
  • Ribonuclease VapC30
KeywordsTOXIN/ANTITOXIN / Mycobacteria / addiction module / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Antitoxin VapB-like / Rv0623-like transcription factor / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease VapC30 / Antitoxin VapB30
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, B.-J. / Lee, I.-G. / Lee, S.J.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and functional studies of the Mycobacterium tuberculosis VapBC30 toxin-antitoxin system: implications for the design of novel antimicrobial peptides
Authors: Lee, I.-G. / Lee, S.J. / Chae, S. / Lee, K.Y. / Kim, J.H. / Lee, B.-J.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_reflns_twin / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease VapC30
B: Antitoxin VapB30
E: Ribonuclease VapC30
F: Antitoxin VapB30
C: Ribonuclease VapC30
D: Antitoxin VapB30
G: Ribonuclease VapC30
H: Antitoxin VapB30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,28811
Polymers94,2158
Non-polymers733
Water1,856103
1
A: Ribonuclease VapC30
B: Antitoxin VapB30
C: Ribonuclease VapC30
D: Antitoxin VapB30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1566
Polymers47,1074
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-65 kcal/mol
Surface area13900 Å2
MethodPISA
2
E: Ribonuclease VapC30
F: Antitoxin VapB30
G: Ribonuclease VapC30
H: Antitoxin VapB30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1325
Polymers47,1074
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-57 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.381, 96.381, 232.788
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Ribonuclease VapC30 / RNase VapC30 / Toxin VapC30 / VapC toxin


Mass: 14398.210 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapC30, Rv0624, MTCY20H10.05 / Plasmid: pET21a / Production host: Escherichia coli (E. coli)
References: UniProt: P9WF77, Hydrolases; Acting on ester bonds
#2: Protein
Antitoxin VapB30 / VapB antitoxin


Mass: 9155.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapB30, Rv0623 / Details (production host): pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJ35
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic dihydrate pH 5.6, 1.0M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.515
11-h,-k,l20.485
ReflectionResolution: 2.7→40.66 Å / Num. obs: 35181 / % possible obs: 99.3 % / Redundancy: 7.7 % / Net I/σ(I): 40.96

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.7→40.66 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.37 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23814 1749 5 %RANDOM
Rwork0.20578 ---
obs0.20736 33411 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.666 Å2
Baniso -1Baniso -2Baniso -3
1-24.9 Å20 Å20 Å2
2--24.9 Å20 Å2
3----49.81 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 3 103 5050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195032
X-RAY DIFFRACTIONr_bond_other_d0.0010.024824
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.966820
X-RAY DIFFRACTIONr_angle_other_deg0.755311024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35422.712236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59415796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1331552
X-RAY DIFFRACTIONr_chiral_restr0.0670.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3035.9642584
X-RAY DIFFRACTIONr_mcbond_other4.3035.9642583
X-RAY DIFFRACTIONr_mcangle_it6.6248.9353216
X-RAY DIFFRACTIONr_mcangle_other6.6258.9363217
X-RAY DIFFRACTIONr_scbond_it3.946.2562448
X-RAY DIFFRACTIONr_scbond_other3.9396.2572449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0149.2583605
X-RAY DIFFRACTIONr_long_range_B_refined8.77647.0245791
X-RAY DIFFRACTIONr_long_range_B_other8.77647.0335786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 144 -
Rwork0.317 2382 -
obs--98.75 %

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