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- PDB-3cto: Crystal Structure of M. tuberculosis YefM antitoxin -

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Basic information

Entry
Database: PDB / ID: 3cto
TitleCrystal Structure of M. tuberculosis YefM antitoxin
ComponentsUncharacterized protein Rv3357/MT3465
KeywordsTOXIN INHIBITOR / Homotetramer
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 ...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: 2.5 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
DepositionApr 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
E: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2297
Polymers51,0375
Non-polymers1922
Water1,06359
1
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
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-112 kcal/mol
Surface area15610 Å2
MethodPISA
2
E: Uncharacterized protein Rv3357/MT3465


Theoretical massNumber of molelcules
Total (without water)10,2071
Polymers10,2071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Uncharacterized protein Rv3357/MT3465

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)51,2297
Polymers51,0375
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area8860 Å2
ΔGint-98 kcal/mol
Surface area19370 Å2
MethodPISA
4
E: Uncharacterized protein Rv3357/MT3465

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)51,2297
Polymers51,0375
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-124 kcal/mol
Surface area15950 Å2
MethodPISA
5
E: Uncharacterized protein Rv3357/MT3465

C: Uncharacterized protein Rv3357/MT3465

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


Theoretical massNumber of molelcules
Total (without water)51,2297
Polymers51,0375
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_454-x-1/2,-y,z-1/21
crystal symmetry operation3_545-x,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-83 kcal/mol
Surface area19620 Å2
MethodPISA
6
A: Uncharacterized protein Rv3357/MT3465
hetero molecules

E: 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)51,2297
Polymers51,0375
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_545-x,y-1/2,-z+1/21
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-85 kcal/mol
Surface area21280 Å2
MethodPISA
7
A: Uncharacterized protein Rv3357/MT3465
B: Uncharacterized protein Rv3357/MT3465
D: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8145
Polymers30,6223
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-63 kcal/mol
Surface area13750 Å2
MethodPISA
8
C: Uncharacterized protein Rv3357/MT3465

E: Uncharacterized protein Rv3357/MT3465


Theoretical massNumber of molelcules
Total (without water)20,4152
Polymers20,4152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area660 Å2
ΔGint-9 kcal/mol
Surface area8480 Å2
MethodPISA
9
E: Uncharacterized protein Rv3357/MT3465

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


Theoretical massNumber of molelcules
Total (without water)30,7184
Polymers30,6223
Non-polymers961
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-49 kcal/mol
Surface area11500 Å2
MethodPISA
10
A: Uncharacterized protein Rv3357/MT3465
B: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5113
Polymers20,4152
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-27 kcal/mol
Surface area10600 Å2
MethodPISA
11
E: Uncharacterized protein Rv3357/MT3465

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


Theoretical massNumber of molelcules
Total (without water)30,7184
Polymers30,6223
Non-polymers961
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-36 kcal/mol
Surface area11450 Å2
MethodPISA
12
B: Uncharacterized protein Rv3357/MT3465
D: Uncharacterized protein Rv3357/MT3465
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5113
Polymers20,4152
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-40 kcal/mol
Surface area11060 Å2
MethodPISA
13
A: 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)30,8145
Polymers30,6223
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_545-x,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-51 kcal/mol
Surface area16200 Å2
MethodPISA
14
C: Uncharacterized protein Rv3357/MT3465

E: Uncharacterized protein Rv3357/MT3465


Theoretical massNumber of molelcules
Total (without water)20,4152
Polymers20,4152
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area660 Å2
ΔGint-9 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.003, 64.573, 83.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 5 / Auth seq-ID: 1 - 54

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDLabel seq-ID
1METMETARGARGAA1 - 54
2SERSERSERSERBB2 - 55
3METMETARGARGCC1 - 54
4SERSERSERSERDD2 - 55

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Components

#1: Protein
Uncharacterized protein Rv3357/MT3465 / antitoxin


Mass: 10207.344 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / 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.: 59 / 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: 1.71719 Å3/Da / Density % sol: 28.371336 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% PEG 1000, 0.1M sodium phosphate citrate, 0.5M lithium sulphate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12668 / Num. obs: 12447 / % possible obs: 98.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 8.5 / Num. unique all: 1222 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.95 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.324 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.695 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 605 4.9 %RANDOM
Rwork0.20528 ---
obs0.20767 11809 98.41 %-
all-12447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 10 59 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9563460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18523.008133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98515443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61534
X-RAY DIFFRACTIONr_chiral_restr0.1190.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021955
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21096
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21732
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7861.51631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29222549
X-RAY DIFFRACTIONr_scbond_it2.23831031
X-RAY DIFFRACTIONr_scangle_it3.6774.5911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.10.5
2Bmedium positional0.120.5
3Cmedium positional0.120.5
4Dmedium positional0.120.5
1Aloose positional1.275
2Bloose positional1.15
3Cloose positional1.175
4Dloose positional0.85
1Amedium thermal0.492
2Bmedium thermal0.732
3Cmedium thermal0.392
4Dmedium thermal0.552
1Aloose thermal2.1110
2Bloose thermal3.6710
3Cloose thermal0.8910
4Dloose thermal2.8710
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 57 -
Rwork0.216 833 -
obs--98.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8637-1.68613.45092.0549-2.87128.0163-0.0523-0.5934-0.25750.0227-0.0027-0.04220.21080.11870.055-0.2486-0.02170.0181-0.1926-0.0162-0.225210.22814.80646.443
23.11960.42083.81011.73340.380210.13620.0707-0.68760.14620.2219-0.20880.12740.0932-0.64320.1381-0.2663-0.0210.0184-0.14120.001-0.16864.213.78247.7
30.403-0.13090.62883.7497-2.7498.06080.16160.06680.0996-0.3003-0.08270.2860.2298-0.2811-0.0789-0.1578-0.04920.0176-0.35590.0169-0.1684-0.98326.75615.904
42.44480.4411-1.75382.4797-1.93325.824-0.09340.2610.0465-0.58630.1041-0.1110.63510.008-0.0107-0.15950.01320.0328-0.32030.0137-0.1958-3.21920.95614.794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 571 - 57
2X-RAY DIFFRACTION2BB1 - 572 - 58
3X-RAY DIFFRACTION3CC1 - 571 - 57
4X-RAY DIFFRACTION4DD1 - 572 - 58

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