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- PDB-3srn: STRUCTURAL CHANGES THAT ACCOMPANY THE REDUCED CATALYTIC EFFICIENC... -

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Basic information

Entry
Database: PDB / ID: 3srn
TitleSTRUCTURAL CHANGES THAT ACCOMPANY THE REDUCED CATALYTIC EFFICIENCY OF TWO SEMISYNTHETIC RIBONUCLEASE ANALOGS
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: 2 Å
AuthorsdeMel, V.S.J. / Martin, P.D. / Doscher, M.S. / Edwards, B.F.P.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs.
Authors: deMel, V.S. / Martin, P.D. / Doscher, M.S. / Edwards, B.F.
History
DepositionMay 20, 1991Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Structure summary
Revision 1.4Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)13,8213
Polymers13,7252
Non-polymers961
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-26 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.700, 64.700, 64.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO A 93

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Components

#1: Protein RIBONUCLEASE A


Mass: 12494.965 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: 1230.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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.: 133 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFEATURES OF THE STRUCTURE: 1. IN SPITE OF AN EIGHT-RESIDUE REDUNDANCY BETWEEN RNASE 1 - 118 AND ...FEATURES OF THE STRUCTURE: 1. IN SPITE OF AN EIGHT-RESIDUE REDUNDANCY BETWEEN RNASE 1 - 118 AND RNASE 111 - 124(D121N), NO REDUNDANT STRUCTURE IS SEEN IN THE CRYSTAL. RESIDUES 114 - 118 OF RNASE 1 - 118 AND RESIDUES 111 - 113 OF RNASE 111 - 124(D121N) DO NOT APPEAR IN THE MAP. 2. HIS 119 IS PREDOMINANTLY IN THE CONFORMATION REPORTED BY MARTIN FOR THE PARENT STRUCTURE.
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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growDetails: THE MOTHER LIQUOR WAS 80 PERCENT SATURATED AMMONIUM SULFATE, PH 5.2.
Crystal grow
*PLUS
pH: 5.2 / Method: macro seeding
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionObserved criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 9604 / % possible obs: 84.8 % / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å / Rfactor Rwork: 0.186 / Rfactor obs: 0.186
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 5 133 1089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 9604 / σ(F): 2 / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_plane_restr0.009
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_angle_deg1.7

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