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- PDB-5rsa: COMPARISON OF TWO INDEPENDENTLY REFINED MODELS OF RIBONUCLEASE-A -

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Basic information

Entry
Database: PDB / ID: 5rsa
TitleCOMPARISON OF TWO INDEPENDENTLY REFINED MODELS OF RIBONUCLEASE-A
ComponentsRIBONUCLEASE A
KeywordsHydrolase/RNA / HYDROLASE-RNA Complex
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
DEUTERATED WATER / PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 2 Å
AuthorsWlodawer, A.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Comparison of Two Independently Refined Models of Ribonuclease-A
Authors: Wlodawer, A. / Borkakoti, N. / Moss, D.S. / Howlin, B.
#1: Journal: Biochemistry / Year: 1985
Title: Nuclear Magnetic Resonance and Neutron Diffraction Studies of the Complex of Ribonucleasea with Uridine Vanadate, a Transition-State Analogue
Authors: Borah, B. / Chen, C.-W. / Egan, W. / Miller, M. / Wlodawer, A. / Cohen, J.S.
#2: Journal: Biochemistry / Year: 1983
Title: Structure of Ribonuclease A. Results of Joint Neutron and X-Ray Refinement at 2.0-Angstroms Resolution
Authors: Wlodawer, A. / Sjolin, L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Active Site of Rnase. Neutron Diffraction Study of a Complex with Uridine Vanadate, a Transition-State Analog
Authors: Wlodawer, A. / Miller, M. / Sjolin, L.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution
Authors: Wlodawer, A. / Bott, R. / Sjolin, L.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Hydrogen Exchange in Rnase A. Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#6: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981
Title: Structure of Ribonuclease A. X-Ray and Neutron Refinement
Authors: Wlodawer, A. / Bott, R. / Sjolin, L.
#7: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981
Title: Joint Refinement of Macromolecular Structures with X-Ray and Neutron Single-Crystal Diffraction Data
Authors: Wlodawer, A. / Hendrickson, W.A.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Orientation of Histidine Residues in Rnase A. Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#9: Journal: Acta Crystallogr.,Sect.B / Year: 1980
Title: Studies of Ribonuclease-A by X-Ray and Neutron Diffraction
Authors: Wlodawer, A.
History
DepositionApr 29, 1985Processing site: BNL
SupersessionJul 17, 1985ID: 4RSA
Revision 1.0Jul 17, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Data collection / Non-polymer description / Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Other / Structure summary / Category: pdbx_database_status / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.4Mar 15, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / refine / 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
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

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8032
Polymers13,7081
Non-polymers951
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.180, 38.400, 53.320
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 93 AND 114 ARE CIS-PROLINES.

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Components

#1: Protein RIBONUCLEASE A


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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.25 %
Description: DATA WERE COLLECTED ON DEUTERATED CRYSTALS. THE SOLVENT IS TERTIARY BUTANOL. AMIDE HYDROGENS WHICH EXCHANGED LESS THAN 50 PER CENT ARE ENTERED AS H, OTHERS ARE ENTERED AS D.
Crystal grow
*PLUS
pH: 5.3 / Method: unknown / Details: Wlodawer, A., (1982) J.Biol.Chem., 257, 1325.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein11
20.3 M11NaOH
343 %t-butylalcohol11

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Processing

Refinement
Resolution (Å)Refine-IDRfactor obsNum. reflection obs% reflection obs (%)Diffraction-IDHighest resolution (Å)
2-10X-RAY DIFFRACTION0.159770895.61
NEUTRON DIFFRACTION0.18341325122
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 128 1084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.023
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
Num. reflection obs: 7708 / Rfactor obs: 0.159 / σ(I): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_angle_d0.062
X-RAY DIFFRACTIONo_chiral_restr0.019

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