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- PDB-3oei: Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3... -

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Basic information

Entry
Database: PDB / ID: 3oei
TitleCrystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)
Components
  • (RelJ (Antitoxin Rv3357)) x 2
  • RelK (Toxin Rv3358)
KeywordsToxin / Protein Binding / Toxin-antitoxin systems / Protein-protein complex / Tuberculosis Structural Genomics Consortium / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


: / RNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription ...: / RNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / : / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / : / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Toxin RelK / Antitoxin RelJ / Toxin RelK / Antitoxin RelJ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsMiallau, L. / Cascio, D. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2013
Title: Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes.
Authors: Miallau, L. / Jain, P. / Arbing, M.A. / Cascio, D. / Phan, T. / Ahn, C.J. / Chan, S. / Chernishof, I. / Maxson, M. / Chiang, J. / Jacobs Jr., W.R. / Eisenberg, D.S.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 23, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RelJ (Antitoxin Rv3357)
B: RelJ (Antitoxin Rv3357)
C: RelK (Toxin Rv3358)
D: RelK (Toxin Rv3358)
E: RelJ (Antitoxin Rv3357)
F: RelJ (Antitoxin Rv3357)
G: RelK (Toxin Rv3358)
H: RelK (Toxin Rv3358)
I: RelJ (Antitoxin Rv3357)
J: RelJ (Antitoxin Rv3357)
K: RelK (Toxin Rv3358)
L: RelK (Toxin Rv3358)
M: RelJ (Antitoxin Rv3357)
N: RelJ (Antitoxin Rv3357)
O: RelK (Toxin Rv3358)
P: RelK (Toxin Rv3358)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,26217
Polymers179,07316
Non-polymers1891
Water7,566420
1
A: RelJ (Antitoxin Rv3357)
B: RelJ (Antitoxin Rv3357)
C: RelK (Toxin Rv3358)
D: RelK (Toxin Rv3358)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9515
Polymers44,7624
Non-polymers1891
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-64 kcal/mol
Surface area16310 Å2
MethodPISA
2
E: RelJ (Antitoxin Rv3357)
F: RelJ (Antitoxin Rv3357)
G: RelK (Toxin Rv3358)
H: RelK (Toxin Rv3358)


Theoretical massNumber of molelcules
Total (without water)44,7884
Polymers44,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-62 kcal/mol
Surface area15720 Å2
MethodPISA
3
I: RelJ (Antitoxin Rv3357)
J: RelJ (Antitoxin Rv3357)
K: RelK (Toxin Rv3358)
L: RelK (Toxin Rv3358)


Theoretical massNumber of molelcules
Total (without water)44,7624
Polymers44,7624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-69 kcal/mol
Surface area15700 Å2
MethodPISA
4
M: RelJ (Antitoxin Rv3357)
N: RelJ (Antitoxin Rv3357)
O: RelK (Toxin Rv3358)
P: RelK (Toxin Rv3358)


Theoretical massNumber of molelcules
Total (without water)44,7624
Polymers44,7624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-66 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.219, 187.512, 113.881
Angle α, β, γ (deg.)90.000, 94.460, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a tetramer. There are 4 biologic unit in the asymmetric unit

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Components

#1: Protein
RelJ (Antitoxin Rv3357)


Mass: 10876.147 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3357, MT3465, MTV004.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P65067, UniProt: P9WF25*PLUS
#2: Protein
RelK (Toxin Rv3358)


Mass: 11504.714 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3358, MT3466, MTV004.15 / Production host: Escherichia coli (E. coli)
References: UniProt: P64528, UniProt: P9WF09*PLUS, Hydrolases; Acting on ester bonds
#3: Protein RelJ (Antitoxin Rv3357)


Mass: 10889.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3357, MT3465, MTV004.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P65067, UniProt: P9WF25*PLUS
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% 2-propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% PEG 4000, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.145→100 Å / Num. obs: 86296 / % possible obs: 89.8 % / Observed criterion σ(I): -2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.066 / Χ2: 1.012 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.232.10.40387300.80590.4
2.23-2.322.10.32586660.90991
2.32-2.422.10.24687140.84191.1
2.42-2.552.20.1987490.91691.3
2.55-2.712.20.15287441.04291.2
2.71-2.922.20.11487161.17791.1
2.92-3.212.30.0987331.14190.4
3.21-3.682.30.06985721.11589.4
3.68-4.632.20.04584781.04887.9
4.63-1002.40.03181941.05784.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_403refinement
PDB_EXTRACT3.1data extraction
Adxvdata processing
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G5O

3g5o


Resolution: 2.145→40.506 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.3 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 4136 5.02 %
Rwork0.2031 --
obs0.2058 82315 85.6 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.226 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 117.03 Å2 / Biso mean: 39.8962 Å2 / Biso min: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1-6.9827 Å2-0 Å20.2787 Å2
2---7.7038 Å20 Å2
3---0.7211 Å2
Refinement stepCycle: LAST / Resolution: 2.145→40.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11046 0 13 420 11479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811338
X-RAY DIFFRACTIONf_angle_d1.0415318
X-RAY DIFFRACTIONf_chiral_restr0.0731603
X-RAY DIFFRACTIONf_plane_restr0.0052031
X-RAY DIFFRACTIONf_dihedral_angle_d15.0144323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1452-2.16960.32041180.26092259237775
2.1696-2.19510.3581410.24022393253478
2.1951-2.22190.29481350.23782466260180
2.2219-2.250.34751080.23772404251281
2.25-2.27960.31341090.24532456256580
2.2796-2.31090.32981190.22562539265882
2.3109-2.34390.28841220.23452599272184
2.3439-2.37890.29311290.22242525265484
2.3789-2.4160.30671570.21332535269284
2.416-2.45560.2931410.21352612275386
2.4556-2.4980.2421450.20592652279787
2.498-2.54340.30231410.21552581272286
2.5434-2.59230.27551380.2152661279987
2.5923-2.64520.30951480.23272698284688
2.6452-2.70270.30211620.22812584274688
2.7027-2.76560.30441370.24562697283488
2.7656-2.83470.2871470.22272721286889
2.8347-2.91130.26451400.21832667280789
2.9113-2.9970.30411620.21452756291889
2.997-3.09370.29141310.21272697282889
3.0937-3.20420.26491410.21122715285689
3.2042-3.33240.25061490.21362686283589
3.3324-3.4840.23951530.22744289789
3.484-3.66760.23861490.18922660280989
3.6676-3.89720.21561390.18612728286789
3.8972-4.19780.23911310.18282712284388
4.1978-4.61970.22081350.17152630276587
4.6197-5.2870.19611380.1692719285788
5.287-6.65620.27621460.21942607275386
6.6562-40.51280.18851250.17652476260179

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