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- PDB-5hjz: Structure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 5hjz
TitleStructure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA
Components
  • Endoribonuclease MazF9
  • RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')
Keywordshydrolase/rna / toxin-antitoxin system / MazF / hydrolase-rna complex
Function / homology
Function and homology information


modulation by symbiont of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
RNA / RNA (> 10) / Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsYen, T.J. / Brennan, R.G.
CitationJournal: To Be Published
Title: Structure of M. tuberculosis MazF-mt1 (Rv2801c) 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 MazF9
B: Endoribonuclease MazF9
C: RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)29,3653
Polymers29,3653
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-12 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.799, 68.542, 80.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoribonuclease MazF9 / Toxin MazF9 / mRNA interferase MazF-mt1


Mass: 12976.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF9, mazF-mt1, Rv2801c / Production host: Escherichia coli (E. coli)
References: UniProt: P71650, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')


Mass: 3411.091 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.: 150 / 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: 1.81 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG1500, 0.1 M MMT buffer

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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: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15533 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.04 / Rrim(I) all: 0.097 / Χ2: 1.13 / Net I/av σ(I): 21.931 / Net I/σ(I): 7.5 / Num. measured all: 90794
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.40.4727740.9480.2220.5230.85299.5
2.01-2.055.60.4227340.9390.1940.4660.87699.9
2.05-2.095.80.3967560.9630.180.4360.849100
2.09-2.135.90.3397720.9620.1520.3720.889100
2.13-2.1860.287740.9780.1260.3080.928100
2.18-2.2360.2667390.9730.1190.2920.939100
2.23-2.2960.2357840.9740.1050.2571100
2.29-2.3560.2117530.9810.0950.2321.002100
2.35-2.4260.27690.9840.0890.220.987100
2.42-2.495.90.1737580.9870.0780.190.978100
2.49-2.5860.1627730.9850.0730.1781.038100
2.58-2.695.90.137650.9910.0580.1431.076100
2.69-2.815.90.1257830.990.0560.1381.123100
2.81-2.965.90.0987750.9940.0440.1071.184100
2.96-3.145.90.0867700.9950.0390.0941.318100
3.14-3.395.90.0797810.9950.0360.0871.601100
3.39-3.735.90.0687910.9970.0310.0741.931100
3.73-4.265.80.057970.9970.0230.0561.577100
4.26-5.375.80.0398060.9990.0180.0431.26100
5.37-505.40.0348790.9990.0160.0381.10299.9

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Processing

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

Resolution: 1.976→34.923 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1548 10 %
Rwork0.2061 13930 -
obs0.2085 15478 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.96 Å2 / Biso mean: 25.3823 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 1.976→34.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 82 0 150 1983
Biso mean---31.69 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031857
X-RAY DIFFRACTIONf_angle_d0.622534
X-RAY DIFFRACTIONf_chiral_restr0.023314
X-RAY DIFFRACTIONf_plane_restr0.004318
X-RAY DIFFRACTIONf_dihedral_angle_d13.192712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9763-2.04010.27071310.23161180131193
2.0401-2.1130.27631380.221612391377100
2.113-2.19760.26241370.211112441381100
2.1976-2.29760.20921410.209512651406100
2.2976-2.41870.29931380.203512371375100
2.4187-2.57020.22641410.220612641405100
2.5702-2.76860.24251410.211512701411100
2.7686-3.0470.24011400.217512651405100
3.047-3.48760.22761430.215712871430100
3.4876-4.39260.20411450.175912991444100
4.3926-34.92880.21061530.206513801533100

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