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- PDB-1ssc: THE 1.6 ANGSTROMS STRUCTURE OF A SEMISYNTHETIC RIBONUCLEASE CRYST... -

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Basic information

Entry
Database: PDB / ID: 1ssc
TitleTHE 1.6 ANGSTROMS STRUCTURE OF A SEMISYNTHETIC RIBONUCLEASE CRYSTALLIZED FROM AQUEOUS ETHANOL. COMPARISON WITH CRYSTALS FROM SALT SOLUTIONS AND WITH RNASE A FROM AQUEOUS ALCOHOL SOLUTIONS
Components(RIBONUCLEASE A) x 2
KeywordsENDONUCLEASE
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
PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDe Mel, V.S.J. / Doscher, M.S. / Martin, P.D. / Rodier, F. / Edwards, B.F.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: 1.6 A structure of semisynthetic ribonuclease crystallized from aqueous ethanol. Comparison with crystals from salt solutions and with ribonuclease A from aqueous alcohol solutions.
Authors: de Mel, S.J. / Doscher, M.S. / Martin, P.D. / Rodier, F. / 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.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: The Refined Crystal Structure of Fully Active Semisynthetic Ribonuclease At 1.8-A Resolution.
Authors: Martin, P.D. / Doscher, M.S. / Edwards, B.F.P.
History
DepositionOct 5, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)13,7073
Polymers13,6122
Non-polymers951
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-19 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.360, 38.340, 53.550
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 93

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Components

#1: Protein RIBONUCLEASE A


Mass: 12380.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P61823
#2: Protein/peptide RIBONUCLEASE A


Mass: 1231.375 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44 %
Crystal grow
*PLUS
pH: 5.3 / Method: seeding
Components of the solutions
*PLUS
Conc.: 43 %(v/v) / Common name: aqueous ethanol

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Data collection

Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 12742 / % possible obs: 72 % / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.67 Å / % possible obs: 54 %

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
FRODOmodel building
X-PLORphasing
RefinementRfactor obs: 0.166 / Highest resolution: 2 Å
Details: THE CLOSE CONTACT BETWEEN THE ASP 83 OD2 AND ARG 85 NH2 IS DUE TO WEAK DENSITY AND DISORDER ASSOCIATED WITH THE ARG 85 RESIDUE.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 5 95 1043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_deg / Dev ideal: 1.7

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