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- PDB-5hkc: Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in... -

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Basic information

Entry
Database: PDB / ID: 5hkc
TitleCrystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with 8-mer RNA
Components
  • Endoribonuclease MazF6
  • RNA (5'-R(*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*A)-3')
KeywordsHYDROLASE/RNA / Toxin-antitoxin system / MazF / HYDROLASE-RNA complex
Function / homology
Function and homology information


positive regulation of growth / symbiont-mediated perturbation of host process / negative regulation of growth / rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / DNA binding / extracellular region
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / Endoribonuclease MazF6 / Endoribonuclease MazF6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsYen, T.J. / Brennan, R.G.
CitationJournal: To Be Published
Title: Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with 8-mer RNA
Authors: Yen, T.J. / Brennan, R.G.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease MazF6
B: Endoribonuclease MazF6
C: RNA (5'-R(*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)26,9623
Polymers26,9623
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-19 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.269, 38.798, 69.178
Angle α, β, γ (deg.)90.000, 107.300, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-270-

HOH

21B-256-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETchain AAA1 - 1141 - 114
2VALVALchain BBB2 - 1142 - 114

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Components

#1: Protein Endoribonuclease MazF6 / Toxin MazF6 / mRNA interferase MazF6


Mass: 12257.037 Da / Num. of mol.: 2 / Mutation: T52D, F62D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: mazF6, MT2046 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WII2, UniProt: P9WII3*PLUS, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: RNA chain RNA (5'-R(*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*A)-3')


Mass: 2447.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 27052 / % possible obs: 95.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.034 / Rrim(I) all: 0.061 / Χ2: 0.934 / Net I/av σ(I): 16.141 / Net I/σ(I): 10.9 / Num. measured all: 74834
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.712.70.45813560.7230.3340.570.78198.2
1.71-1.742.70.39913550.7960.2890.4950.79698.6
1.74-1.772.70.3214130.8750.2320.3970.78998.4
1.77-1.812.70.27613290.9070.1970.3410.898
1.81-1.852.70.2414060.9150.1720.2970.83297.9
1.85-1.892.70.1813600.9480.130.2230.84797.7
1.89-1.942.70.15713830.9610.1120.1930.89797.8
1.94-1.992.70.11713320.9790.0830.1450.83897.2
1.99-2.052.70.10313780.9810.0720.1260.94797.3
2.05-2.122.80.08513460.9880.060.1050.9597
2.12-2.192.80.07213830.990.0510.0890.9297.1
2.19-2.282.80.06713560.9910.0470.0820.96796.2
2.28-2.382.80.06513260.9910.0450.0791.04995.3
2.38-2.512.80.06113420.9920.0420.0741.1895.7
2.51-2.672.80.06213440.9920.0420.0751.13395
2.67-2.872.80.06513370.9910.0440.0791.17794.5
2.87-3.162.90.05613400.9930.0370.0671.03794.5
3.16-3.622.90.04713280.9950.0310.0560.95792.9
3.62-4.562.90.03313160.9970.0220.040.85391.5
4.56-502.90.02913220.9980.0190.0350.8988.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MazF-mt3

Resolution: 1.68→33.453 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 2008 7.42 %
Rwork0.2007 25041 -
obs0.203 27049 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.94 Å2 / Biso mean: 25.6438 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.68→33.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 39 39 160 1942
Biso mean--31.25 34.78 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071768
X-RAY DIFFRACTIONf_angle_d1.1792426
X-RAY DIFFRACTIONf_chiral_restr0.049307
X-RAY DIFFRACTIONf_plane_restr0.007308
X-RAY DIFFRACTIONf_dihedral_angle_d11.731658
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A938X-RAY DIFFRACTION11.014TORSIONAL
12B938X-RAY DIFFRACTION11.014TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.679-1.7210.2821490.26181744189395
1.721-1.76750.26951520.23031835198798
1.7675-1.81950.29811360.22691800193698
1.8195-1.87820.27811490.20931811196098
1.8782-1.94540.25961490.20411835198498
1.9454-2.02330.23221440.20991793193798
2.0233-2.11530.23871370.20041801193897
2.1153-2.22680.25241460.19611793193997
2.2268-2.36630.21571420.18891783192596
2.3663-2.54890.22481380.19481798193695
2.5489-2.80530.23681480.21221783193195
2.8053-3.2110.22661390.20561764190394
3.211-4.04440.21591370.18961745188292
4.0444-33.45980.21631420.19331756189890

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