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- PDB-6etr: Atomic resolution structure of RNase A (data collection 8) -

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Basic information

Entry
Database: PDB / ID: 6etr
TitleAtomic resolution structure of RNase A (data collection 8)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Raman microspectroscopy / ribonuclease / atomic resolution / radiation damage / photodamage
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsCaterino, M. / Vergara, A. / Merlino, A.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Raman-markers of X-ray radiation damage of proteins.
Authors: Vergara, A. / Caterino, M. / Merlino, A.
History
DepositionOct 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8894
Polymers13,7081
Non-polymers1803
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint8 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.125, 37.971, 52.541
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 39.68 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: Free-interface diffusion of a 10 uL of 30 mg ml-1 protein solution, 20 mM sodium citrate at pH 5.3 agaist 10 ul isopropanol 99.9% isopropanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 32132 / % possible obs: 88.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.29 / % possible all: 86.5

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF3

1kf3


Resolution: 1.17→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2314 1251 -
Rwork0.1611 --
obs0.1734 30534 86.5 %
Displacement parametersBiso mean: 19.16 Å2
Refinement stepCycle: LAST / Resolution: 1.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 12 144 1107

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