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- PDB-6ybc: RNASE 3/1 version2 phosphate complex -

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Basic information

Entry
Database: PDB / ID: 6ybc
TitleRNASE 3/1 version2 phosphate complex
ComponentsRNASE 3/1 version2
KeywordsHYDROLASE / RNASE 3/1 version2 / PANCREATIC RIBONUCLEASE
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsFernandez-Millan, P. / Prats-Ejarque, G. / Vazquez-Monteagudo, S. / Boix, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF2015-66007-P Spain
CitationJournal: Front Mol Biosci / Year: 2022
Title: Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras.
Authors: Fernandez-Millan, P. / Vazquez-Monteagudo, S. / Boix, E. / Prats-Ejarque, G.
History
DepositionMar 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNASE 3/1 version2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6537
Polymers16,0861
Non-polymers5676
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-20 kcal/mol
Surface area8700 Å2
Unit cell
Length a, b, c (Å)43.160, 61.740, 51.521
Angle α, β, γ (deg.)90.000, 106.461, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

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Components

#1: Protein RNASE 3/1 version2


Mass: 16086.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate, pH 6.5 and 1 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792568 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792568 Å / Relative weight: 1
ReflectionResolution: 1.48→38.58 Å / Num. obs: 21301 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 1.48→1.62 Å / Num. unique obs: 1062 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K11

2k11


Resolution: 1.49→38.58 Å / SU ML: 0.1422 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.3484
RfactorNum. reflection% reflection
Rfree0.1931 1999 9.39 %
Rwork0.1471 --
obs0.1514 21291 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.78 Å2
Refinement stepCycle: LAST / Resolution: 1.49→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 31 147 1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781277
X-RAY DIFFRACTIONf_angle_d0.97171745
X-RAY DIFFRACTIONf_chiral_restr0.0782166
X-RAY DIFFRACTIONf_plane_restr0.0081233
X-RAY DIFFRACTIONf_dihedral_angle_d25.6249745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.23311430.1621386X-RAY DIFFRACTION99.61
1.52-1.560.22521410.1431353X-RAY DIFFRACTION99.14
1.56-1.610.17181430.14091384X-RAY DIFFRACTION99.48
1.61-1.660.19861430.13891371X-RAY DIFFRACTION99.34
1.66-1.720.20471410.13341363X-RAY DIFFRACTION99.08
1.72-1.790.20181430.13411380X-RAY DIFFRACTION99.35
1.79-1.870.19111420.13151363X-RAY DIFFRACTION99.08
1.87-1.970.20071410.13461366X-RAY DIFFRACTION98.56
1.97-2.090.16381420.13391364X-RAY DIFFRACTION99.14
2.09-2.250.17351420.13161382X-RAY DIFFRACTION99.28
2.25-2.480.20241430.1391389X-RAY DIFFRACTION99.55
2.48-2.840.16841440.1461381X-RAY DIFFRACTION99.74
2.84-3.580.17921440.15371396X-RAY DIFFRACTION99.74
3.58-38.580.21851470.16731414X-RAY DIFFRACTION99.24

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