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- PDB-6ybe: RNASE 3/1 version2 -

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Basic information

Entry
Database: PDB / ID: 6ybe
TitleRNASE 3/1 version2
ComponentsRNASE 3/1 version2
KeywordsHYDROLASE / RNASE 3/1 version2 / PANCREATIC RIBONUCLEASE
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNASE 3/1 version2


Theoretical massNumber of molelcules
Total (without water)16,0861
Polymers16,0861
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8380 Å2
Unit cell
Length a, b, c (Å)43.210, 61.770, 51.346
Angle α, β, γ (deg.)90.000, 106.883, 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-319-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium acetate pH 5 and 1 M sodium chloride

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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: 1.12→38.45 Å / Num. obs: 43663 / % possible obs: 92.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 10.73 Å2 / CC1/2: 0.996 / Net I/σ(I): 16.9
Reflection shellResolution: 1.12→1.14 Å / Num. unique obs: 2247 / CC1/2: 0.966 / % possible all: 90.9

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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: 1.14→38.45 Å / SU ML: 0.076 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 15.4717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1655 1906 4.38 %
Rwork0.1514 41630 -
obs0.152 43536 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.14→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 179 1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711261
X-RAY DIFFRACTIONf_angle_d1.01041722
X-RAY DIFFRACTIONf_chiral_restr0.0832167
X-RAY DIFFRACTIONf_plane_restr0.0079239
X-RAY DIFFRACTIONf_dihedral_angle_d27.231746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.170.17021320.13552873X-RAY DIFFRACTION90.21
1.17-1.20.181320.13132897X-RAY DIFFRACTION90.28
1.2-1.240.15641310.13072853X-RAY DIFFRACTION89.61
1.24-1.280.1421330.12912928X-RAY DIFFRACTION91.81
1.28-1.320.16741350.13262922X-RAY DIFFRACTION91.83
1.32-1.370.1611340.12852951X-RAY DIFFRACTION92.48
1.37-1.440.15311350.14012928X-RAY DIFFRACTION90.81
1.44-1.510.15741350.13432954X-RAY DIFFRACTION92.73
1.51-1.610.17261390.13523024X-RAY DIFFRACTION93.86
1.61-1.730.17081370.13992993X-RAY DIFFRACTION93.66
1.73-1.910.15771400.14823067X-RAY DIFFRACTION94.97
1.91-2.180.1591410.14923054X-RAY DIFFRACTION95.12
2.18-2.750.16591390.16393064X-RAY DIFFRACTION94.85
2.75-38.450.17281430.16763122X-RAY DIFFRACTION95.3

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