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- PDB-1ssb: A STRUCTURAL INVESTIGATION OF CATALYTICALLY MODIFIED F12OL AND F1... -

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Basic information

Entry
Database: PDB / ID: 1ssb
TitleA STRUCTURAL INVESTIGATION OF CATALYTICALLY MODIFIED F12OL AND F12OY SEMISYNTHETIC RIBONUCLEASES
Components(RIBONUCLEASE A) x 2
KeywordsHYDROLASE(ENDORIBONUCLEASE)
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. / Doscher, M.S. / Glinn, M.A. / Martin, P.D. / Ram, M.L. / Edwards, B.F.P.
Citation
Journal: Protein Sci. / Year: 1994
Title: Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
Authors: deMel, V.S. / Doscher, M.S. / Glinn, M.A. / Martin, P.D. / Ram, M.L. / Edwards, B.F.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Structural Changes that Accompany the Reduced Catalytic Efficiency of Two Semisynthetic Ribonuclease Analogs
Authors: De Mel, V.S.J. / Martin, P.D. / Doscher, M.S. / Edwards, B.F.P.
History
DepositionAug 3, 1993Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 6, 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)14,6673
Polymers14,5712
Non-polymers961
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-30 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.150, 68.150, 65.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CYS A 72 - TYR A 73 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 93

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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 (cattle) / Tissue: PANCREAS / References: UniProt: P61823
#2: Protein/peptide RIBONUCLEASE A


Mass: 1520.618 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.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFEATURES OF THE STRUCTURE IN SPITE OF AN EIGHT-RESIDUE REDUNDANCY BETWEEN RNASE 1 - 118 AND RNASE ...FEATURES OF THE STRUCTURE IN SPITE OF AN EIGHT-RESIDUE REDUNDANCY BETWEEN RNASE 1 - 118 AND RNASE 111 - 124(F120Y), NO REDUNDANT STRUCTURE IS SEEN IN THE CRYSTAL. RESIDUES 114 - 118 OF RNASE 1 - 118 AND RESIDUES 111 - 113 OF RNASE 111 - 124(F120Y) DO NOT APPEAR IN THE MAP.
Has protein modificationY
Nonpolymer detailsA TOTAL OF 94 WATER MOLECULES WERE INCLUDED. A SULFATE ANION OCCURS IN THE ACTIVE SITE AND WAS ALSO ...A TOTAL OF 94 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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growDetails: THE MOTHER LIQUOR WAS 80 % SATURATED AMMONIUM SULFATE, PH 5.2.
Crystal grow
*PLUS
pH: 5.7 / 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 %sat1reservoir(NH4)2SO4
50.1 Mammonium acetate1reservoir
65 mM1,10-phenanthroline1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 5 Å / Num. obs: 11776 / % possible obs: 94.6 % / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→7 Å /
RfactorNum. reflection
Rwork0.184 -
obs0.184 11776
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 5 95 1052
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
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.9

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