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- PDB-9ikd: The apo structure of the MazF-mt3 toxin -

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Basic information

Entry
Database: PDB / ID: 9ikd
TitleThe apo structure of the MazF-mt3 toxin
ComponentsEndoribonuclease MazF6
KeywordsTOXIN / toxin-antitoxin system / MazF / Mycobacterium tuberculosis
Function / homologymRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / DNA binding / Endoribonuclease MazF6
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsXie, W. / Jiang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Long Dynamic beta 1-beta 2 Loops in M. tb MazF Toxins Affect the Interaction Modes and Strengths of the Toxin-Antitoxin Pairs.
Authors: Tang, Z. / Jiang, P. / Xie, W.
History
DepositionJun 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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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: Endoribonuclease MazF6
F: Endoribonuclease MazF6
G: Endoribonuclease MazF6
H: Endoribonuclease MazF6
I: Endoribonuclease MazF6
J: Endoribonuclease MazF6
L: Endoribonuclease MazF6
K: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)152,05912
Polymers152,05912
Non-polymers00
Water00
1
A: Endoribonuclease MazF6
G: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoribonuclease MazF6
I: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoribonuclease MazF6
E: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoribonuclease MazF6
F: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: Endoribonuclease MazF6
J: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L: Endoribonuclease MazF6
K: Endoribonuclease MazF6


Theoretical massNumber of molelcules
Total (without water)25,3432
Polymers25,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.795, 110.795, 271.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 4 through 9 and (name N...
d_2ens_1(chain "B" and ((resid 4 through 9 and (name N...
d_3ens_1(chain "C" and ((resid 4 through 9 and (name N...
d_4ens_1(chain "D" and ((resid 4 through 9 and (name N...
d_5ens_1(chain "E" and ((resid 4 through 9 and (name N...
d_6ens_1(chain "F" and ((resid 4 through 9 and (name N...
d_7ens_1(chain "G" and ((resid 4 through 9 and (name N...
d_8ens_1(chain "H" and ((resid 4 through 9 and (name N...
d_9ens_1(chain "I" and ((resid 4 through 9 and (name N...
d_10ens_1(chain "J" and ((resid 4 through 9 and (name N...
d_11ens_1(chain "K" and ((resid 4 through 9 and (name N...
d_12ens_1(chain "L" and ((resid 4 through 9 and (name N...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTRPTRPAA4 - 108 - 14
d_12PROPROTHRTHRAA26 - 8330 - 87
d_13LYSLYSLEULEUAA86 - 11490 - 118
d_21SERSERTRPTRPBB4 - 108 - 14
d_22PROPROTHRTHRBB26 - 8330 - 87
d_23LYSLYSLEULEUBB86 - 11490 - 118
d_31SERSERTRPTRPCC4 - 108 - 14
d_32PROPROTHRTHRCC26 - 8330 - 87
d_33LYSLYSLEULEUCC86 - 11490 - 118
d_41SERSERTRPTRPDD4 - 108 - 14
d_42PROPROTHRTHRDD26 - 8330 - 87
d_43LYSLYSLEULEUDD86 - 11490 - 118
d_51SERSERTRPTRPEE4 - 108 - 14
d_52PROPROTHRTHREE26 - 8330 - 87
d_53LYSLYSLEULEUEE86 - 11490 - 118
d_61SERSERTRPTRPFF4 - 108 - 14
d_62PROPROTHRTHRFF26 - 8330 - 87
d_63LYSLYSLEULEUFF86 - 11490 - 118
d_71SERSERTRPTRPGG4 - 108 - 14
d_72PROPROTHRTHRGG26 - 8330 - 87
d_73LYSLYSLEULEUGG86 - 11490 - 118
d_81SERSERTRPTRPHH4 - 108 - 14
d_82PROPROTHRTHRHH26 - 8330 - 87
d_83LYSLYSLEULEUHH86 - 11490 - 118
d_91SERSERTRPTRPII4 - 108 - 14
d_92PROPROTHRTHRII26 - 8330 - 87
d_93LYSLYSLEULEUII86 - 11490 - 118
d_101SERSERTRPTRPJJ4 - 108 - 14
d_102PROPROTHRTHRJJ26 - 8330 - 87
d_103LYSLYSLEULEUJJ86 - 11490 - 118
d_111SERSERTRPTRPKL4 - 108 - 14
d_112PROPROTHRTHRKL26 - 8330 - 87
d_113LYSLYSLEULEUKL86 - 11490 - 118
d_121SERSERTRPTRPLK4 - 108 - 14
d_122PROPROTHRTHRLK26 - 8330 - 87
d_123LYSLYSLEULEULK86 - 11490 - 118

NCS oper:
IDCodeMatrixVector
1given(0.997150887564, 0.0011142997469, -0.075424570038), (-0.00261327198597, -0.9987803771, -0.04930445344), (-0.0753875204452, 0.0493610844245, -0.995931827539)-2.64150139584, -14.8885198766, -66.2512076242
2given(0.76374245174, 0.432807099418, 0.478931604828), (-0.350943098966, -0.344314565747, 0.870796429197), (0.541790004243, -0.833141941393, -0.11107698589)-7.2886925081, -13.2199968306, -64.4410503099
3given(0.704052959279, 0.525780723211, 0.477351088436), (0.351435082711, 0.326141618023, -0.877567676953), (-0.617092224202, 0.785612039173, 0.0448431793637)-4.49276528986, -0.830809999729, 0.103886172421
4given(-0.293250374084, 0.833693294997, 0.4679313069), (0.417568457971, 0.551988179028, -0.721765635869), (-0.860023721189, -0.016264688461, -0.509994763602)21.7477338313, -54.407497436, -30.5053660297
5given(-0.194536004561, 0.834762503048, 0.515099317059), (-0.43316076409, -0.544263526872, 0.71843508111), (0.880072437577, -0.0833593235438, 0.467465215599)20.6679953152, 40.9999555819, -36.2497149666
6given(-0.843031614158, 0.454247176734, 0.288022915686), (0.413097221514, 0.203882825505, 0.887571112104), (0.344453745963, 0.867231973519, -0.359527914074)54.5017729996, -0.210123092477, -26.566026625
7given(0.240766673294, 0.966787122217, -0.0857558706251), (0.62054515123, -0.221270204937, -0.752305264963), (-0.74629426121, 0.127914646241, -0.653209552105)-16.4036511908, -39.1929369767, -22.0988989705
8given(-0.862836088135, 0.386370901277, 0.325931605798), (-0.445649505128, -0.277144910083, -0.851226889492), (-0.238559014902, -0.879720538274, 0.411316631013)53.7810528036, -12.6515334176, -43.9715915273
9given(0.168399899966, 0.229912425935, 0.958531037626), (-0.865198069069, -0.431458237178, 0.255491860637), (0.47230686526, -0.87234400667, 0.126262262994)-1.32786252178, 14.4138124471, -46.0273517068
10given(0.703225347489, 0.480496218962, -0.524020509342), (0.6207894822, -0.0557208857282, 0.781994630214), (0.346546576146, -0.875224866224, -0.337471338197)-18.8180046859, -36.3017938568, -23.5822629718
11given(-0.549541608625, -0.0451087545783, 0.83424769742), (-0.305231428955, 0.940355409079, -0.150218106078), (-0.777713183101, -0.337189716444, -0.530533033803)32.8189842541, -22.2954976611, 4.96469559386

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Components

#1: Protein
Endoribonuclease MazF6 / Toxin MazF6 / mRNA interferase MazF6


Mass: 12671.578 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: mazF6, MT2046 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WII2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1-1.5 M NaCl, 0.1 M NaOAc pH4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.32→75.27 Å / Num. obs: 24018 / % possible obs: 92.7 % / Redundancy: 24.2 % / Biso Wilson estimate: 106 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Net I/σ(I): 18.4
Reflection shellResolution: 3.32→3.5 Å / Rmerge(I) obs: 1.309 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2906 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→75.27 Å / SU ML: 0.4319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 1156 4.86 %
Rwork0.2422 22639 -
obs0.2439 23795 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.79 Å2
Refinement stepCycle: LAST / Resolution: 3.32→75.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9020 0 0 0 9020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039132
X-RAY DIFFRACTIONf_angle_d0.609512561
X-RAY DIFFRACTIONf_chiral_restr0.04731657
X-RAY DIFFRACTIONf_plane_restr0.0061614
X-RAY DIFFRACTIONf_dihedral_angle_d11.3253169
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.211989532738
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.217367257779
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.263453129696
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.24975332278
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.406862234375
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.264603283714
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.235353594921
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.282883593356
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.387142493466
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.406600551397
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.47738462762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.470.38181220.31462226X-RAY DIFFRACTION74.28
3.47-3.640.31441480.28222781X-RAY DIFFRACTION98.92
3.68-3.870.38261160.27652489X-RAY DIFFRACTION98.67
3.91-4.180.27611460.23892672X-RAY DIFFRACTION98.95
4.18-4.610.26391520.2143043X-RAY DIFFRACTION99.5
4.61-5.270.24521610.21573049X-RAY DIFFRACTION99.72
5.27-6.640.27231610.26053086X-RAY DIFFRACTION99.66
6.64-75.270.26731500.23743293X-RAY DIFFRACTION99.22

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