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- PDB-7bxy: mRNA interferase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 7bxy
TitlemRNA interferase from Bacillus cereus
ComponentsmRNA interferase
KeywordsHYDROLASE / mRNA interferase
Function / homologymRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / mRNA interferase
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKang, S.M.
Funding support1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)
CitationJournal: To Be Published
Title: mRNA interferase from Bacillus cereus
Authors: Kang, S.M.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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

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Assembly

Deposited unit
A: mRNA interferase


Theoretical massNumber of molelcules
Total (without water)12,9901
Polymers12,9901
Non-polymers00
Water1,54986
1
A: mRNA interferase

A: mRNA interferase


Theoretical massNumber of molelcules
Total (without water)25,9802
Polymers25,9802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+7/31
Buried area2890 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.648, 60.648, 76.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein mRNA interferase


Mass: 12990.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: ndoA, A6E21_26500, A9485_14350, ACS95_12765, AT267_05875, AT272_01830, AT274_27885, AWW71_24810, B1995_17895, B2J90_01430, B4077_0233, B4079_4082, B4082_4620, B4088_0025, BACERE00183_00384, ...Gene: ndoA, A6E21_26500, A9485_14350, ACS95_12765, AT267_05875, AT272_01830, AT274_27885, AWW71_24810, B1995_17895, B2J90_01430, B4077_0233, B4079_4082, B4082_4620, B4088_0025, BACERE00183_00384, BACERE00184_01021, BACERE00185_00762, BACERE00191_00063, BC05F1_00266, BC067498_00234, BC141101_05148, BC2903_38150, BcrFT9_00246, BCRIVMBC845_00478, BG03_4879, BHL25_17845, BHL27_05940, BHL35_14900, BJR07_22055, BKK44_23145, BLX06_29915, C6Y54_07400, CEW46_16915, CJ306_01400, CN284_23940, CN290_26025, CN307_30430, CN415_21275, CN431_00035, CN490_24970, CN909_30810, CN950_27630, CN980_28290, CNQ78_21155, COC58_26245, COD14_00505, COD18_21020, COD86_27525, COD94_16985, COE18_25465, COI98_15170, COJ27_20485, COJ45_22815, CON05_27270, CON22_19380, CQZ91_26535, CV717_25730, CW365_02650, DR116_0030920, E0M29_20970, EDC93_113101, F2Y18_23305, FC691_26725, FC692_09555, FC695_10780, FHG65_28905, SAMN04487767_13815, SAMN05878494_5153, TU62_23120, TU68_19155, WR52_01230
Production host: Escherichia coli (E. coli)
References: UniProt: A0A063CKW3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.899995 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 12876 / % possible obs: 99.3 % / Redundancy: 10.57 % / Biso Wilson estimate: 37.95 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.74
Reflection shellResolution: 1.98→2.1 Å / Num. unique obs: 3402 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→43.25 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.4902
RfactorNum. reflection% reflection
Rfree0.2254 1165 9.95 %
Rwork0.1894 --
obs0.1931 11713 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.22 Å2
Refinement stepCycle: LAST / Resolution: 1.98→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 0 86 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078922
X-RAY DIFFRACTIONf_angle_d1.10771246
X-RAY DIFFRACTIONf_chiral_restr0.0676152
X-RAY DIFFRACTIONf_plane_restr0.0052159
X-RAY DIFFRACTIONf_dihedral_angle_d8.6661570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.25311370.2071220X-RAY DIFFRACTION94.24
2.07-2.170.21841440.20591303X-RAY DIFFRACTION100
2.17-2.310.22461430.19981318X-RAY DIFFRACTION99.93
2.31-2.490.24021440.20671302X-RAY DIFFRACTION100
2.49-2.740.24841440.21061315X-RAY DIFFRACTION100
2.74-3.140.25721490.22391331X-RAY DIFFRACTION100
3.14-3.950.25211470.18721340X-RAY DIFFRACTION100
3.95-43.250.18681570.16491419X-RAY DIFFRACTION100

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