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- PDB-1ub4: crystal structure of MazEF complex -

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Basic information

Entry
Database: PDB / ID: 1ub4
Titlecrystal structure of MazEF complex
Components
  • MazE protein
  • MazF protein
KeywordsDNA BINDING PROTEIN / toxin / antidote / programmed cell death / post-segregation / addiction module / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity ...toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity / negative regulation of cell growth / regulation of translation / double-stranded DNA binding / defense response to virus / regulation of DNA-templated transcription / protein-containing complex binding / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding
Similarity search - Function
: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SH3 type barrels. - #110 / SpoVT-AbrB domain superfamily / mRNA interferase PemK-like ...: / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SH3 type barrels. - #110 / SpoVT-AbrB domain superfamily / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Ribbon / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease toxin MazF / Antitoxin MazE / Antitoxin MazE / Endoribonuclease toxin MazF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsKamada, K. / Hanaoka, F. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal Structure of the MazE/MazF Complex. Molecular Bases of Antidote-Toxin Recognition
Authors: Kamada, K. / Hanaoka, F. / Burley, S.K.
History
DepositionMar 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MazF protein
B: MazF protein
C: MazE protein


Theoretical massNumber of molelcules
Total (without water)33,6213
Polymers33,6213
Non-polymers00
Water3,585199
1
A: MazF protein
B: MazF protein
C: MazE protein

A: MazF protein
B: MazF protein
C: MazE protein


Theoretical massNumber of molelcules
Total (without water)67,2416
Polymers67,2416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area14530 Å2
ΔGint-98 kcal/mol
Surface area26130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.591, 116.717, 76.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1199-

HOH

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Components

#1: Protein MazF protein


Mass: 11980.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mazF / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33645, UniProt: P0AE70*PLUS
#2: Protein MazE protein


Mass: 9659.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MazE / Plasmid: modified pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18534, UniProt: P0AE72*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: NaAcetate, NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH4.5
32 M1reservoirNaCl
415 %(v/v)glycerol1reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97899 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 18, 2001 / Details: flat cylindrically bent mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 37150 / Num. obs: 37150 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.7 % / Biso Wilson estimate: 22.9 Å2 / Limit h max: 43 / Limit h min: 0 / Limit k max: 68 / Limit k min: 0 / Limit l max: 45 / Limit l min: 0 / Observed criterion F max: 2136482.77 / Observed criterion F min: 3.5 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 26.7
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 13.6 / Num. unique all: 1230 / Rsym value: 0.187 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 805050 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→21.11 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2596 7.1 %RANDOM
Rwork0.21 ---
all0.251 37117 --
obs0.248 36629 98.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 44.9037 Å2 / ksol: 0.381541 e/Å3
Displacement parametersBiso max: 64.08 Å2 / Biso mean: 26.98 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2--2.36 Å20 Å2
3----6.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Luzzati d res high-1.7
Refinement stepCycle: LAST / Resolution: 1.7→21.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 199 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg24.4
X-RAY DIFFRACTIONc_torsion_impr_deg0.95
X-RAY DIFFRACTIONc_mcbond_it1.5941.5
X-RAY DIFFRACTIONc_mcangle_it2.6462.5
X-RAY DIFFRACTIONc_scbond_it2.2052
X-RAY DIFFRACTIONc_scangle_it3.3033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.7-1.780.2573086.90.2341810.0154626448997
1.78-1.870.2783036.80.2441590.0164587446297.3
1.87-1.990.2493136.90.21742180.0144633453197.8
1.99-2.140.2533156.90.2142420.0144625455798.5
2.14-2.360.2293377.40.20642020.0124624453998.2
2.36-2.70.2433477.60.21842460.0134657459398.6
2.7-3.390.2273136.70.20943340.0134689464799.1
3.39-21.110.2173607.50.20344510.0114861481199
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 22 Å / % reflection Rfree: 7 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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