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- PDB-3ev0: Crystal Structure of Ribonuclease A in 70% Dimethyl Sulfoxide -

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Basic information

Entry
Database: PDB / ID: 3ev0
TitleCrystal Structure of Ribonuclease A in 70% Dimethyl Sulfoxide
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNAse / organic solvents / multiple solvent crystal structures / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å
AuthorsDechene, M. / Wink, G. / Smith, M. / Swartz, P. / Mattos, C.
CitationJournal: Proteins / Year: 2009
Title: Multiple solvent crystal structures of ribonuclease A: An assessment of the method
Authors: Dechene, M. / Wink, G. / Smith, M. / Swartz, P. / Mattos, C.
History
DepositionOct 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,19812
Polymers27,4172
Non-polymers78110
Water3,549197
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9434
Polymers13,7081
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2558
Polymers13,7081
Non-polymers5477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.965, 32.641, 72.908
Angle α, β, γ (deg.)90.000, 90.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-953-

HOH

21B-1076-

HOH

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, sodium citrate, pH 5.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 22635 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.069 / Χ2: 3.717
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.76-1.822.90.41121401.73294
1.82-1.93.20.36922521.896.3
1.9-1.983.40.26822201.99396.9
1.98-2.093.40.19922272.21696.6
2.09-2.223.30.14822602.44797.4
2.22-2.393.40.12222772.49197.2
2.39-2.633.40.09422792.74997.8
2.63-3.013.40.07122884.53698
3.01-3.793.20.05223277.31298.4
3.79-502.90.043236510.2896.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.76→41.28 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 2185 9.1 %
Rwork0.208 --
obs-22032 91.7 %
Solvent computationBsol: 39.487 Å2
Displacement parametersBiso max: 81.21 Å2 / Biso mean: 30.356 Å2 / Biso min: 10.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å2-1.335 Å2
2---2.174 Å20 Å2
3----0.635 Å2
Refinement stepCycle: LAST / Resolution: 1.76→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 40 197 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.338
X-RAY DIFFRACTIONc_mcbond_it1.4861.5
X-RAY DIFFRACTIONc_scbond_it1.9992
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scangle_it2.9342.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dms.paramdms.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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