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- PDB-8hvj: The structure of the E. coli mRNA endoonuclease YiCC -

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Basic information

Entry
Database: PDB / ID: 8hvj
TitleThe structure of the E. coli mRNA endoonuclease YiCC
ComponentsUPF0701 protein YicC
KeywordsHYDROLASE / mRNA endoonuclease / yicC / mRNA metabolism
Function / homology
Function and homology information


RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / cytosol
Similarity search - Function
Conserved hypothetical protein CHP00255 / YicC-like, N-terminal / Domain of unknown function DUF1732 / Endoribonuclease YicC-like, N-terminal region / Endoribonuclease YicC-like, C-terminal
Similarity search - Domain/homology
Endoribonuclease YicC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å
AuthorsXie, W. / Hunag, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271322 China
CitationJournal: To Be Published
Title: The structure of the E. coli mRNA endoonuclease YiCC
Authors: Xie, W. / Hunag, L.
History
DepositionDec 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0701 protein YicC
B: UPF0701 protein YicC
C: UPF0701 protein YicC


Theoretical massNumber of molelcules
Total (without water)99,6513
Polymers99,6513
Non-polymers00
Water00
1
A: UPF0701 protein YicC
B: UPF0701 protein YicC
C: UPF0701 protein YicC

A: UPF0701 protein YicC
B: UPF0701 protein YicC
C: UPF0701 protein YicC


Theoretical massNumber of molelcules
Total (without water)199,3016
Polymers199,3016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area18600 Å2
ΔGint-59 kcal/mol
Surface area84360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.208, 77.158, 102.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein UPF0701 protein YicC


Mass: 33216.902 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yicC, b3644, JW3619 / Production host: Escherichia coli (E. coli) / References: UniProt: P23839

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24.5% PEG 3350, 0.15M Ammonium sulfate, 0.1M HEPES pH7.5, 5mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.05→102.6 Å / Num. obs: 9159 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.9
Reflection shellResolution: 4.05→4.27 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.63 / Num. unique obs: 1309 / CC1/2: 0.821 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.05→102.596 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.87 / SU B: 0.032 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 1.122 / ESU R Free: 1.346
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3847 434 4.753 %
Rwork0.3206 8698 -
all0.324 --
obs-9132 99.88 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 196.331 Å2
Baniso -1Baniso -2Baniso -3
1-5.022 Å2-0 Å20 Å2
2---2.367 Å2-0 Å2
3----2.655 Å2
Refinement stepCycle: LAST / Resolution: 4.05→102.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6285 0 0 0 6285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.05-4.1540.459340.347622X-RAY DIFFRACTION100
4.154-4.2670.411350.337613X-RAY DIFFRACTION100
4.267-4.3910.476300.323580X-RAY DIFFRACTION100
4.391-4.5260.427260.323598X-RAY DIFFRACTION100
4.526-4.6740.363290.31561X-RAY DIFFRACTION100
4.674-4.8370.394250.313543X-RAY DIFFRACTION100
4.837-5.020.425230.319532X-RAY DIFFRACTION100
5.02-5.2240.411190.361507X-RAY DIFFRACTION100
5.224-5.4560.522340.38494X-RAY DIFFRACTION100
5.456-5.7210.612230.396464X-RAY DIFFRACTION100
5.721-6.030.439260.378454X-RAY DIFFRACTION99.7921
6.03-6.3940.49190.39432X-RAY DIFFRACTION100
6.394-6.8330.398210.359393X-RAY DIFFRACTION100
6.833-7.3780.579130.336384X-RAY DIFFRACTION100
7.378-8.0780.258130.286351X-RAY DIFFRACTION100
8.078-9.0250.423150.277318X-RAY DIFFRACTION100
9.025-10.4080.356170.214289X-RAY DIFFRACTION100
10.408-12.7140.187110.205251X-RAY DIFFRACTION100
12.714-17.8440.197130.335191X-RAY DIFFRACTION100
17.844-102.5960.42880.783121X-RAY DIFFRACTION92.8058

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