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- PDB-7y7o: Crystal structure of metallo-endoribonuclease YbeY from Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 7y7o
TitleCrystal structure of metallo-endoribonuclease YbeY from Staphylococcus aureus
ComponentsEndoribonuclease YbeY
KeywordsHYDROLASE / RNA / endoribonuclease / metalloprotein / zinc
Function / homology
Function and homology information


RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Endoribonuclease YbeY
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLee, J. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Microbiol Biotechnol. / Year: 2023
Title: Crystal Structure of the Metallo-Endoribonuclease YbeY from Staphylococcus aureus.
Authors: Lee, J. / Jo, I. / Kwon, A.R. / Ha, N.C.
History
DepositionJun 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease YbeY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3214
Polymers18,8721
Non-polymers4503
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-19 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.663, 100.663, 50.187
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Endoribonuclease YbeY


Mass: 18871.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: ybeY, SAV1570 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P67136, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.89 Å3/Da / Density % sol: 71.26 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate (pH 5.5), 40% (v/v) PEG 400, 1 mM Zinc sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28176 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28176 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22303 / % possible obs: 96.6 % / Redundancy: 21.1 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.012 / Rrim(I) all: 0.055 / Net I/σ(I): 56
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 14.6 / Num. unique obs: 1017 / CC1/2: 0.988 / CC star: 0.997 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→43.59 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 21.3305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 2002 8.98 %
Rwork0.1967 20296 -
obs0.1993 22298 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 27 54 1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681261
X-RAY DIFFRACTIONf_angle_d0.89941702
X-RAY DIFFRACTIONf_chiral_restr0.0568179
X-RAY DIFFRACTIONf_plane_restr0.0077224
X-RAY DIFFRACTIONf_dihedral_angle_d18.7362166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.23111340.21511329X-RAY DIFFRACTION89.04
1.95-20.20571360.20881374X-RAY DIFFRACTION93.04
2-2.060.29161400.20691432X-RAY DIFFRACTION95.5
2.06-2.120.24561390.20461434X-RAY DIFFRACTION96.21
2.12-2.20.2681420.20551433X-RAY DIFFRACTION96.8
2.2-2.290.23791390.19571453X-RAY DIFFRACTION95.96
2.29-2.390.20651390.19931450X-RAY DIFFRACTION96.65
2.39-2.520.26381430.20871445X-RAY DIFFRACTION97.36
2.52-2.680.2181440.20561469X-RAY DIFFRACTION97.94
2.68-2.880.2431510.22671480X-RAY DIFFRACTION98.31
2.88-3.170.25061420.22571450X-RAY DIFFRACTION97.79
3.17-3.630.22331450.19651505X-RAY DIFFRACTION98.68
3.63-4.570.18621490.15981508X-RAY DIFFRACTION99.1
4.58-43.590.20251590.17791534X-RAY DIFFRACTION99.12

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