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- PDB-4srn: STRUCTURAL CHANGES THAT ACCOMPANY THE REDUCED CATALYTIC EFFICIENC... -

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Basic information

Entry
Database: PDB / ID: 4srn
TitleSTRUCTURAL CHANGES THAT ACCOMPANY THE REDUCED CATALYTIC EFFICIENCY OF TWO SEMISYNTHETIC RIBONUCLEASE ANALOGS
Components(RIBONUCLEASE APancreatic ribonuclease family) x 2
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (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

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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)13,7783
Polymers13,6822
Non-polymers961
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-30 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.730, 64.730, 64.920
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 / Pancreatic ribonuclease family


Mass: 12494.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Protein/peptide RIBONUCLEASE A / Pancreatic ribonuclease family


Mass: 1187.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P61823
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 111 / 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(D121A), NO REDUNDANT STRUCTURE IS SEEN IN THE CRYSTAL. RESIDUES 114 - 118 OF RNASE 1 - 118 AND RESIDUES 111 - 113 OF RNASE 111 - 124(D121A) DO NOT APPEAR IN THE MAP. 2. HIS 119 IS PREDOMINANTLY IN THE CONFORMATION REPORTED BY MARTIN FOR THE PARENT STRUCTURE.
Nonpolymer detailsA TOTAL OF 111 WATER MOLECULES WERE INCLUDED. A SULFATE ANION OCCURS IN THE ACTIVE SITE AND WAS ...A TOTAL OF 111 WATER MOLECULES WERE INCLUDED. 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: 2.87 Å3/Da / Density % sol: 57.12 %
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: 10236 / % possible obs: 90.7 % / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å / Rfactor Rwork: 0.172 / Rfactor obs: 0.172
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 5 111 1064
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: 10236 / σ(F): 2 / Rfactor obs: 0.172
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_deg1.8

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