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- PDB-3euz: Crystal Structure of Ribonuclease A in 50% Dimethylformamide -

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Basic information

Entry
Database: PDB / ID: 3euz
TitleCrystal Structure of Ribonuclease A in 50% Dimethylformamide
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
DIMETHYLFORMAMIDE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 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 1.4Oct 16, 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
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4903
Polymers27,4172
Non-polymers731
Water4,360242
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7812
Polymers13,7081
Non-polymers731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.683, 32.793, 72.608
Angle α, β, γ (deg.)90.000, 90.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1000-

HOH

21B-216-

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-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 43.73 %
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: 1.78→35 Å / Num. obs: 20712 / % possible obs: 88.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.041 / Χ2: 2.882
Reflection shell
Resolution (Å)Redundancy (%)Num. unique all% possible allRmerge(I) obsΧ2
1.78-1.8413100
1.84-1.922.9220795.50.2021.848
1.92-23.5229499.80.1722.155
2-2.113.6229599.80.1322.372
2.11-2.243.7232299.90.1032.696
2.24-2.423.6231999.20.0792.434
2.42-2.663.5230299.40.062.501
2.66-3.043.52300990.0413.371
3.04-3.833.3230597.70.0284.325
3.83-353.3236596.90.0214.25

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.84→29.55 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.229 2006 9.6 %
Rwork0.194 --
obs-20351 96.9 %
Solvent computationBsol: 29.19 Å2
Displacement parametersBiso max: 70.5 Å2 / Biso mean: 28.817 Å2 / Biso min: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.824 Å20 Å2-2.181 Å2
2---0.379 Å20 Å2
3----2.445 Å2
Refinement stepCycle: LAST / Resolution: 1.84→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 5 242 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.212
X-RAY DIFFRACTIONc_mcbond_it1.4311.5
X-RAY DIFFRACTIONc_scbond_it2.0132
X-RAY DIFFRACTIONc_mcangle_it2.3162
X-RAY DIFFRACTIONc_scangle_it3.0792.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dmf.paramdmf.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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