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- PDB-7rsa: STRUCTURE OF PHOSPHATE-FREE RIBONUCLEASE A REFINED AT 1.26 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 7rsa
TitleSTRUCTURE OF PHOSPHATE-FREE RIBONUCLEASE A REFINED AT 1.26 ANGSTROMS
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE (PHOSPHORIC DIESTER)
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
TERTIARY-BUTYL ALCOHOL / Ribonuclease pancreatic / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.26 Å
AuthorsWlodawer, A. / Gilliland, G.L.
Citation
Journal: Biochemistry / Year: 1988
Title: Structure of phosphate-free ribonuclease A refined at 1.26 A.
Authors: Wlodawer, A. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L.
#1: Journal: Proteins / Year: 1986
Title: Multiple Conformations of Amino Acid Residues in Ribonuclease A
Authors: Svensson, L.A. / Sjolin, L. / Gilliland, G.L. / Finzel, B.C. / Wlodawer, A.
#2: 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.
#3: 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.
History
DepositionJun 10, 1988Processing site: BNL
Revision 1.0Oct 9, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / refine / struct_conn / struct_sheet_order / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _refine.details
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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)13,7822
Polymers13,7081
Non-polymers741
Water3,387188
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. / 2: SEE REMARK 4.

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell line: S2 / Organ: PANCREAS
References: UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal grow
*PLUS
pH: 5.3 / Method: unknown / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein11
20.3 Msodium hydroxide11
343 %(v/v)MPD11

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Data collection

Reflection
*PLUS
Highest resolution: 1.26 Å / Num. all: 30947 / Num. obs: 25732 / Num. measured all: 129694 / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.15 / Highest resolution: 1.26 Å
Details: SOME WATER MOLECULES ARE CLOSER THAN 2.8 ANGSTROMS FROM OTHER WATER MOLECULES. THEY MAY REPRESENT ALTERNATELY OCCUPIED SITES OR SEPARATE NETWORKS. SEE THE PAPER CITED ON THE *JRNL* RECORDS ...Details: SOME WATER MOLECULES ARE CLOSER THAN 2.8 ANGSTROMS FROM OTHER WATER MOLECULES. THEY MAY REPRESENT ALTERNATELY OCCUPIED SITES OR SEPARATE NETWORKS. SEE THE PAPER CITED ON THE *JRNL* RECORDS ABOVE FOR MORE DETAILS. SOME ATOMS IN RESIDUES 7 AND 31 HAVE AN OCCUPANCY LESS THAN 1.0. THESE ATOMS WERE POORLY DEFINED IN THE ELECTRON DENSITY AND THEIR OCCUPANCY WAS LOWERED.
Refinement stepCycle: LAST / Highest resolution: 1.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 188 1144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 23398 / σ(F): 2 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_plane_restr0.017
X-RAY DIFFRACTIONp_chiral_restr0.188

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