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- PDB-1rbb: THE CRYSTAL STRUCTURE OF RIBONUCLEASE B AT 2.5-ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1rbb
TitleTHE CRYSTAL STRUCTURE OF RIBONUCLEASE B AT 2.5-ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE B
KeywordsHYDROLASE (NUCLEIC ACID / RNA)
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWilliams, R.L. / Greene, S.M. / McPherson, A.
Citation
Journal: J.Biol.Chem. / Year: 1987
Title: The crystal structure of ribonuclease B at 2.5-A resolution.
Authors: Williams, R.L. / Greene, S.M. / McPherson, A.
#1: Journal: J.Biol.Chem. / Year: 1982
Title: Preliminary Diffraction Data for Crystals of Ribonucleasesa Andb and Their Complexes with Deoxy(Pa)4 and Deoxy(Pa)6
Authors: Brayer, G.D. / McPherson, A.
History
DepositionSep 14, 1987Processing site: BNL
Revision 1.0Jul 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 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 B
B: RIBONUCLEASE B


Theoretical massNumber of molelcules
Total (without water)27,4172
Polymers27,4172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.810, 33.360, 73.600
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 93 AND 114 OF BOTH CHAINS ARE CIS PROLINES. / 2: SEE REMARK 3.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.56472, 0.79491, -0.22183), (-0.82517, -0.54828, 0.13595), (-0.01356, 0.25984, 0.96566)
Vector: 130.06239, 70.78307, 23.91357)

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Components

#1: Protein RIBONUCLEASE B


Mass: 13708.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22 M1dropNH4OH
318 %(w/w)PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementRfactor Rwork: 0.218 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 0 1900
Refinement
*PLUS
Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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