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- PDB-1rsm: THE 2-ANGSTROMS RESOLUTION STRUCTURE OF A THERMOSTABLE RIBONUCLEA... -

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Basic information

Entry
Database: PDB / ID: 1rsm
TitleTHE 2-ANGSTROMS RESOLUTION STRUCTURE OF A THERMOSTABLE RIBONUCLEASE A CHEMICALLY CROSS-LINKED BETWEEN LYSINE RESIDUES 7 AND 41
ComponentsRIBONUCLEASE APancreatic ribonuclease family
KeywordsHYDROLASE (NUCLEIC ACID / RNA)
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
DINITROPHENYLENE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWeber, P.C. / Sheriff, S. / Ohlendorf, D.H. / Finzel, B.C. / Salemme, F.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: The 2-A resolution structure of a thermostable ribonuclease A chemically cross-linked between lysine residues 7 and 41.
Authors: Weber, P.C. / Sheriff, S. / Ohlendorf, D.H. / Finzel, B.C. / Salemme, F.R.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Preliminary Crystallographic Data for Cross-Linked (Lysine7-Lysine41)-Ribonuclease A
Authors: Weber, P.C. / Salemme, F.R. / Lin, S.H. / Konishi, Y. / Scheraga, H.A.
#2: Journal: Biochemistry / Year: 1984
Title: Influence of an Extrinsic Cross-Link on the Folding Pathway of Ribonuclease A. Conformational and Thermodynamic Analysis of Cross-Linked (Lysine7-Lysine41)-Ribonuclease A
Authors: Lin, S.H. / Konishi, Y. / Denton, M.E. / Scheraga, H.A.
#3: Journal: Biochemistry / Year: 1983
Title: Structure of Ribonuclease A. Results of Joint Neutron and X-Ray Refinement at 2.0-Angstroms Resolutions
Authors: Wlodawer, A. / Sjolin, L.
History
DepositionAug 27, 1985-
Revision 1.0Jan 21, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF ...SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF SHEET S1, RESIDUES 88 AND 89 *BULGE OUT*. IN ORDER TO REPRESENT THIS BREAK IN STRAND 2, TWO SHEETS (S1A AND S1B) ARE DEFINED BELOW. STRANDS 1 AND 3 OF *SHEETS* S1A AND S1B ARE, THEREFORE, IDENTICAL AND STRAND 2 DIFFERS. SHEET S2 COMPRISES FOUR STRANDS. RESIDUE 120 DOES NOT PROPERLY BELONG IN STRAND 4 OF SHEET S2. IN ORDER TO REPRESENT THIS BREAK IN STRAND 4, TWO SHEETS (S2A AND S2B) ARE DEFINED BELOW. STRANDS 1,2,3 OF *SHEETS* S2A AND S2B ARE, THEREFORE, IDENTICAL AND STRAND 4 DIFFERS.

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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)13,8762
Polymers13,7081
Non-polymers1681
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.050, 41.260, 75.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 93 AND 114 ARE CIS-PROLINES.

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Components

#1: Protein RIBONUCLEASE A / Pancreatic ribonuclease family


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: S2 / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-NIN / DINITROPHENYLENE / 1,3-Dinitrobenzene


Mass: 168.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal grow
*PLUS
Temperature: 7 ℃ / pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
Conc.: 30 %(v/v) / Common name: ethanol
Details: 50mM-Tris-HCl(pH7.5) and 50 mM-imidazole(pH8.0) are also suitable

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Num. obs: 8301 / Rmerge(I) obs: 0.081 / Num. measured all: 10701

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2 Å / σ(I): 1 /
RfactorNum. reflection
Rwork0.184 -
obs-7853
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 12 75 1038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.024
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å / σ(I): 1 / Highest resolution: 2 Å / Num. reflection obs: 7853 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d0.038
X-RAY DIFFRACTIONo_planar_d0.044
X-RAY DIFFRACTIONo_chiral_restr0.283

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