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- PDB-5hk0: Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in comple... -

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Basic information

Entry
Database: PDB / ID: 5hk0
TitleCrystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA
Components
  • Endoribonuclease MazF6
  • RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-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 / RNA (> 10) / Endoribonuclease MazF6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYen, T.J. / Brennan, R.G.
CitationJournal: To Be Published
Title: Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,8316
Polymers55,8316
Non-polymers00
Water3,099172
1
A: Endoribonuclease MazF6
B: Endoribonuclease MazF6
E: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,9153
Polymers27,9153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endoribonuclease MazF6
D: Endoribonuclease MazF6
F: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,9153
Polymers27,9153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.338, 68.338, 88.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 12275.140 Da / Num. of mol.: 4
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: RNA chain RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Mass: 3365.011 Da / Num. of mol.: 2
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.: 172 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.8 M Ammonium sulfate, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.25→50 Å / Num. obs: 21890 / % possible obs: 99.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.054 / Χ2: 1.019 / Net I/av σ(I): 19.525 / Net I/σ(I): 12.4 / Num. measured all: 61859
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.292.50.4310850.87895.9
2.29-2.332.70.4210770.8599.3
2.33-2.382.70.38411050.86299.6
2.38-2.422.80.32911060.86199.9
2.42-2.482.80.26910690.91100
2.48-2.532.80.24811170.923100
2.53-2.62.80.28910901.44199.9
2.6-2.672.80.21410940.998100
2.67-2.752.80.17310940.894100
2.75-2.832.80.13811180.967100
2.83-2.942.80.10810681.015100
2.94-3.052.90.08410991.074100
3.05-3.192.90.07111070.979100
3.19-3.362.90.05610881.067100
3.36-3.572.90.04310961.087100
3.57-3.852.90.0411021.025100
3.85-4.232.90.03111001.151100
4.23-4.852.90.02610891.16999.9
4.85-6.12.90.02710911.09399.6
6.1-502.90.02310951.06298.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B. subtilis MazF

Resolution: 2.25→49.173 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.31 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2568 1996 9.12 %
Rwork0.2121 19847 -
obs0.2156 21877 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.13 Å2 / Biso mean: 40.1914 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 2.25→49.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 138 39 172 3597
Biso mean--44.34 40.15 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023444
X-RAY DIFFRACTIONf_angle_d0.7214729
X-RAY DIFFRACTIONf_chiral_restr0.027609
X-RAY DIFFRACTIONf_plane_restr0.004576
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711284
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 (%)
2.2513-2.30760.36351540.28341397155187
2.3076-2.370.39361420.28951437157991
2.37-2.43970.32681410.27981397153891
2.4397-2.51850.32691340.25681431156591
2.5185-2.60840.33931400.27041428156891
2.6084-2.71280.3381440.25771399154391
2.7128-2.83620.371380.2451439157791
2.8362-2.98570.28431480.23811387153590
2.9857-3.17260.27551310.22721437156892
3.1726-3.41740.26691400.20251453159391
3.4174-3.76090.25641480.19291387153590
3.7609-4.30420.21061390.17261430156991
4.3042-5.41940.16531480.16191402155090
5.4194-34.17290.2341440.20961423156791

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