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- PDB-1srn: THE REFINED CRYSTAL STRUCTURE OF A FULLY ACTIVE SEMISYNTHETIC RIB... -

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Basic information

Entry
Database: PDB / ID: 1srn
TitleTHE REFINED CRYSTAL STRUCTURE OF A FULLY ACTIVE SEMISYNTHETIC RIBONUCLEASE AT 1.8 ANGSTROMS RESOLUTION
Components(RIBONUCLEASE A) x 2
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: 1.8 Å
AuthorsMartin, P.D. / Doscher, M.S. / Edwards, B.F.P.
CitationJournal: J.Biol.Chem. / Year: 1987
Title: The refined crystal structure of a fully active semisynthetic ribonuclease at 1.8-A resolution.
Authors: Martin, P.D. / Doscher, M.S. / Edwards, B.F.
History
DepositionOct 5, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6783
Polymers14,5822
Non-polymers961
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-29 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 67.680, 65.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUE 93 IS A CIS-PROLINE.

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Components

#1: Protein RIBONUCLEASE A


Mass: 13050.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Protein/peptide RIBONUCLEASE A


Mass: 1531.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P61823
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFEATURES OF THE STRUCTURE 1. IN SPITE OF AN EIGHT-RESIDUE REDUNANCY BETWEEN RNASE 1 - 118 AND RNASE ...FEATURES OF THE STRUCTURE 1. IN SPITE OF AN EIGHT-RESIDUE REDUNANCY BETWEEN RNASE 1 - 118 AND RNASE 111 - 124, NO REDUNDANT STRUCTURE IS SEEN IN THE CRYSTAL. RESIDUES 114 - 118 OF RNASE 1 - 118 AND RESIDUES 111 - 113 OF RNASE 111 - 124 DO NOT APPEAR IN THE MAP. 2. HIS 119 IS PREDOMINANTLY IN THE CONFORMATION REPORTED AS A MINOR OCCUPANCY BY BORKAKOTI ET AL. (ACTA CRYSTALLOGR.,SECT. B, V. 38, P. 2210, 1982, PDB ENTRY 1RN3).
Has protein modificationY
Nonpolymer detailsA TOTAL OF 115 WATER MOLECULES WERE INCLUDED IN THE LAST FOUR CYCLES OF REFINEMENT. A SULFATE ANION ...A TOTAL OF 115 WATER MOLECULES WERE INCLUDED IN THE LAST FOUR CYCLES OF REFINEMENT. A SULFATE ANION OCCURS IN THE ACTIVE SITE AND WAS ALSO REFINED AS PART OF THE STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growDetails: THE MOTHER LIQUOR WAS 80 PER CENT SATURATED AMMONIUM SULFATE, PH 5.2.
Crystal grow
*PLUS
pH: 5.7 / Method: macro seeding / Details: took Sasaki et al., 1979a from original paper
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

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rmerge(I) obs: 2
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2.3 Å / % possible obs: 57 % / Num. possible: 8542 / Num. unique obs: 4828

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.204 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 115 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 121117 / σ(I): 2 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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