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- PDB-1a5p: C[40,95]A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 1a5p
TitleC[40,95]A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A
ComponentsRIBONUCLEASE APancreatic ribonuclease
KeywordsHYDROLASE / HYDROLASE (NUCLEIC ACID / RNA)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA phosphodiester bond hydrolysis / ribonuclease activity / lyase activity / nucleic acid binding / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease family signature. / Ribonuclease A-domain / Pancreatic ribonuclease / Pancreatic ribonuclease / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Ribonuclease A, active site / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.6 Å
AuthorsPearson, M.A. / Karplus, P.A. / Dodge, R.W. / Laity, J.H. / Scheraga, H.A.
CitationJournal: Protein Sci. / Year: 1998
Title: Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A.
Authors: Pearson, M.A. / Karplus, P.A. / Dodge, R.W. / Laity, J.H. / Scheraga, H.A.
History
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7402
Polymers13,6441
Non-polymers961
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)64.600, 64.600, 65.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBONUCLEASE A / Pancreatic ribonuclease


Mass: 13644.195 Da / Num. of mol.: 1 / Mutation: C40A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / Plasmid: PSJII [C40A,C95A] / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) PLYSS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM CACODYLATE PH 6.0, 2.2 M CSCL, AND 1.5 M AMM SO4. THEN IT WAS SOAKED IN 100 MM CACODYLATE PH 6.0, 80% AMM SO4 FOR 24 HOURS TO REMOVE THE CS IONS.
Crystal grow
*PLUS
pH: 5.7 / Method: macro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.95 mMRNase1-1181drop
29.9 mMRNase111-1241drop
33.0 M1reservoirCsCl
428 %satammonium sulfate1reservoir
50.1 Mammonium acetate1reservoir
65 mM1,10-phenanthroline1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 7, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 20673 / % possible obs: 97 % / Redundancy: 3.2 % / Rsym value: 0.039 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.317 / % possible all: 89
Reflection
*PLUS
Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.317

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Processing

Software
NameClassification
SDMSdata collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 -4.7 %RANDOM
Rwork0.223 ---
obs0.223 20369 --
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 5 120 1074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.479
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.505
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.341 117
Rwork0.358 2181
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARALLHDG.PROTOPALLHDG.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.505
LS refinement shell
*PLUS
Rfactor obs: 0.358

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