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- PDB-4mdx: Crystal structure of Bacillus subtilis MazF in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 4mdx
TitleCrystal structure of Bacillus subtilis MazF in complex with RNA
Components
  • RNA, mRNA
  • mRNA interferase EndoA
KeywordsHYDROLASE/RNA / Toxin-antitoxin complex / Toxin-mRNA complex / MazF / mRNA interferase / EndoA / YdcE / Toxin / Antitoxin / MazE / HYDROLASE-RNA complex
Function / homology
Function and homology information


rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / DNA binding / RNA binding
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
IODIDE ION / RNA / Endoribonuclease EndoA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSimanshu, D.K. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2013
Title: Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus subtilis.
Authors: Simanshu, D.K. / Yamaguchi, Y. / Park, J.H. / Inouye, M. / Patel, D.J.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA interferase EndoA
B: mRNA interferase EndoA
C: RNA, mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,73210
Polymers28,9483
Non-polymers7847
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-28 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.793, 69.885, 79.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRNA interferase EndoA / Endoribonuclease EndoA / Toxin EndoA / mRNA interferase MazF-bs / MazF-bs


Mass: 13081.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU04660, mazF, ndoA, ydcE / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P96622, Hydrolases; Acting on ester bonds
#2: RNA chain RNA, mRNA


Mass: 2785.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized ssRNA
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium iodide, 20% w/v PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 60026 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.171 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.554.70.53159470.6021100
1.55-1.624.70.39659110.5921100
1.62-1.694.70.31159200.6271100
1.69-1.784.70.20959270.6621100
1.78-1.894.70.15960000.7291100
1.89-2.044.70.11759571.0051100
2.04-2.244.70.10359791.5281100
2.24-2.564.60.09360161.8831100
2.56-3.234.50.06360611.8199.8
3.23-254.60.04763082.274199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.42 Å
Translation2.5 Å48.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.554 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.14 / σ(F): 1.36 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 1998 3.33 %Random
Rwork0.1644 ---
obs0.1648 59959 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.76 Å2 / Biso mean: 18.2771 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 184 7 354 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062084
X-RAY DIFFRACTIONf_angle_d1.0882871
X-RAY DIFFRACTIONf_chiral_restr0.071356
X-RAY DIFFRACTIONf_plane_restr0.005338
X-RAY DIFFRACTIONf_dihedral_angle_d13.722845
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 (%)
1.5001-1.53760.29451350.23324082421799
1.5376-1.57920.20851420.20740844226100
1.5792-1.62570.23841440.192241104254100
1.6257-1.67810.21621430.184540734216100
1.6781-1.73810.20031430.179440944237100
1.7381-1.80770.17381420.164941054247100
1.8077-1.88990.18071380.166741414279100
1.8899-1.98950.17111440.156541034247100
1.9895-2.11410.19861350.154641204255100
2.1141-2.27720.1721440.157941304274100
2.2772-2.50620.17851420.165241624304100
2.5062-2.86830.16241440.166941784322100
2.8683-3.6120.1471480.158641954343100
3.612-24.55750.17291540.151743844538100
Refinement TLS params.Method: refined / Origin x: 0.9071 Å / Origin y: 11.3641 Å / Origin z: 11.6708 Å
111213212223313233
T0.0608 Å2-0.0089 Å20.0033 Å2-0.0584 Å20.0022 Å2--0.0584 Å2
L1.2205 °2-0.404 °20.2726 °2-1.2066 °2-0.2526 °2--0.8395 °2
S0.0002 Å °-0.0363 Å °-0.05 Å °0.0191 Å °0.0078 Å °0.0064 Å °0.0258 Å °-0.0027 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 114
2X-RAY DIFFRACTION1allB0 - 114
3X-RAY DIFFRACTION1allC1 - 9
4X-RAY DIFFRACTION1allA - C1 - 101
5X-RAY DIFFRACTION1allA1 - 204
6X-RAY DIFFRACTION1allA - B1 - 449

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