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- PDB-5hk3: Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in... -

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Basic information

Entry
Database: PDB / ID: 5hk3
TitleCrystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA
Components
  • DNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')
  • Endoribonuclease MazF6
Keywordshydrolase/dna / Toxin-antitoxin system / MazF / hydrolase-dna complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / positive regulation of growth / 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
DNA / DNA (> 10) / Endoribonuclease MazF6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 DNA
Authors: Yen, T.J. / Brennan, R.G.
History
DepositionJan 13, 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: DNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,7193
Polymers27,7193
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.311, 64.244, 73.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 114 / Label seq-ID: 2 - 114

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Endoribonuclease MazF6 / Toxin MazF6 / mRNA interferase MazF-mt3


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 ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF6, mazF-mt3, Rv1991c, MTCY39.28 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WII3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: DNA chain DNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')


Mass: 3205.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris 0.1 M Ammonium acetate 17% PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 32174 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.059 / Rrim(I) all: 0.107 / Χ2: 1.199 / Net I/av σ(I): 14.809 / Net I/σ(I): 14.8 / Num. measured all: 105841
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.592.60.40714050.7780.290.5030.68887.7
1.59-1.623.10.38415910.7740.2640.4690.68298.2
1.62-1.653.30.35116120.8370.2330.4230.679100
1.65-1.683.30.31916140.90.2080.3830.67499.9
1.68-1.723.40.26615900.9160.1720.3180.74100
1.72-1.763.40.22616180.9370.1450.270.81499.9
1.76-1.83.40.19716070.9570.1270.2350.84199.9
1.8-1.853.40.16116370.9680.1030.1920.901100
1.85-1.93.40.14616170.9770.0920.1731.00399.9
1.9-1.973.40.12416210.9780.0790.1481.147100
1.97-2.043.40.11416120.980.0720.1361.293100
2.04-2.123.40.10716210.9810.0670.1261.37499.9
2.12-2.213.50.10116350.9840.0640.121.48499.9
2.21-2.333.40.09216340.9840.0580.1091.488100
2.33-2.483.50.08816440.9830.0550.1041.47999.9
2.48-2.673.40.07916410.9830.050.0941.45499.8
2.67-2.943.40.08116590.9840.0510.0971.68599.8
2.94-3.363.30.07416620.9860.0480.0891.60499.7
3.36-4.2330.07416500.9870.0510.091.78898.1
4.23-502.60.07815040.9820.0570.0972.32283.5

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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: 1.56→26.526 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1998 6.22 %
Rwork0.1915 30113 -
obs0.1926 32111 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.72 Å2 / Biso mean: 24.4332 Å2 / Biso min: 9.1 Å2
Refinement stepCycle: final / Resolution: 1.56→26.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 95 0 182 1913
Biso mean---36.8 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061762
X-RAY DIFFRACTIONf_angle_d1.072427
X-RAY DIFFRACTIONf_chiral_restr0.042308
X-RAY DIFFRACTIONf_plane_restr0.006298
X-RAY DIFFRACTIONf_dihedral_angle_d11.618652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A847X-RAY DIFFRACTION10.539TORSIONAL
12B847X-RAY DIFFRACTION10.539TORSIONAL
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 (%)
1.5599-1.59890.26081250.21671881200686
1.5989-1.64210.25611410.209821392280100
1.6421-1.69050.25181460.192721802326100
1.6905-1.7450.23161410.189921452286100
1.745-1.80740.2091440.18921602304100
1.8074-1.87970.20341430.194121642307100
1.8797-1.96520.19051450.187621722317100
1.9652-2.06880.20311440.171921902334100
2.0688-2.19840.2141450.182521762321100
2.1984-2.3680.21791460.18122042350100
2.368-2.60610.19571450.186421852330100
2.6061-2.98280.22991470.19622172364100
2.9828-3.75630.18271480.18392231237999
3.7563-26.52990.20221380.20492069220788

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