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- PDB-3d55: Crystal structure of M. tuberculosis YefM antitoxin -

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Basic information

Entry
Database: PDB / ID: 3d55
TitleCrystal structure of M. tuberculosis YefM antitoxin
ComponentsUncharacterized protein Rv3357/MT3465
KeywordsTOXIN INHIBITOR / Tetramer / Toxin neutraliser
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc Repressor Mutant - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / Arc Repressor Mutant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Arc Repressor Mutant - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / Arc Repressor Mutant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Antitoxin RelJ / Antitoxin RelJ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsKumar, P. / Issac, B. / Dodson, E.J. / Turkenberg, J.P. / Mande, S.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein
Authors: Kumar, P. / Issac, B. / Dodson, E.J. / Turkenburg, J.P. / Mande, S.C.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 Rv3357/MT3465
B: Uncharacterized protein Rv3357/MT3465
C: Uncharacterized protein Rv3357/MT3465
D: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0226
Polymers40,8294
Non-polymers1922
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-115 kcal/mol
Surface area17390 Å2
MethodPISA
2
A: Uncharacterized protein Rv3357/MT3465
C: Uncharacterized protein Rv3357/MT3465
hetero molecules

B: Uncharacterized protein Rv3357/MT3465
D: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0226
Polymers40,8294
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area7630 Å2
ΔGint-84 kcal/mol
Surface area20810 Å2
MethodPISA
3
D: Uncharacterized protein Rv3357/MT3465
hetero molecules

A: Uncharacterized protein Rv3357/MT3465
B: Uncharacterized protein Rv3357/MT3465
C: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0226
Polymers40,8294
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-78 kcal/mol
Surface area21570 Å2
MethodPISA
4
B: Uncharacterized protein Rv3357/MT3465

D: Uncharacterized protein Rv3357/MT3465
hetero molecules

A: Uncharacterized protein Rv3357/MT3465
C: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0226
Polymers40,8294
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x,y+1/2,-z+1/21
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-78 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.848, 64.776, 83.486
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 Rv3357/MT3465 / Antitoxin


Mass: 10207.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3357, MT3465, MTV004.14 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P65067, UniProt: P9WF25*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 1.0M ammonium sulphate, 0.1M sodium phosphate-citrate, 1% Glycerol, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.13→51.3 Å / Num. all: 19797 / Num. obs: 18793 / % possible obs: 86.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.5
Reflection shellResolution: 2.13→2.23 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1832 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0011refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CTO

3cto


Resolution: 2.13→51.3 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.717 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; THIS IS A TWINNED DATA. THE TWINNING OPERATOR IS (H,K,L) -> (k, -h, l) AND THE TWINNING FRACTION is 0.404.
RfactorNum. reflection% reflectionSelection details
Rfree0.21657 969 4.9 %RANDOM
Rwork0.17959 ---
obs0.18151 17054 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.252 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å2-11.81 Å2-0.21 Å2
2--2.93 Å20 Å2
3----9.37 Å2
Refinement stepCycle: LAST / Resolution: 2.13→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 10 56 2615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0212575
X-RAY DIFFRACTIONr_angle_refined_deg2.4951.9573482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17823.158133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.05915450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7931533
X-RAY DIFFRACTIONr_chiral_restr0.2330.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211970
X-RAY DIFFRACTIONr_mcbond_it1.6871.51600
X-RAY DIFFRACTIONr_mcangle_it2.61622570
X-RAY DIFFRACTIONr_scbond_it4.2933975
X-RAY DIFFRACTIONr_scangle_it6.1594.5912
LS refinement shellResolution: 2.125→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 53 -
Rwork0.157 882 -
obs-1832 63.22 %

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