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- PDB-1rca: STRUCTURE OF THE CRYSTALLINE COMPLEX OF DEOXYCYTIDYLYL-3',5'-GUAN... -

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Basic information

Entry
Database: PDB / ID: 1rca
TitleSTRUCTURE OF THE CRYSTALLINE COMPLEX OF DEOXYCYTIDYLYL-3',5'-GUANOSINE (3',5'-DCPDG) CO-CRYSTALISED WITH RIBONUCLEASE AT 1.9 ANGSTROMS RESOLUTION. RETROBINDING IN PANCREATIC RNASEA IS INDEPENDENT OF MODE OF INHIBITOR INTROMISSION
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE (ENDORIBONUCLEASE)
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
Chem-CGP / PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLisgarten, J.N. / Palmer, R.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution.
Authors: Listgarten, J.N. / Maes, D. / Wyns, L. / Aguilar, C.F. / Palmer, R.A.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Newly Observed Binding Mode in Pancreatic Ribonuclease
Authors: Aguilar, C.F. / Thomas, P.J. / Mills, A. / Moss, D.S. / Palmer, R.A.
#2: Journal: J.Crystallogr.Spectrosc.Res. / Year: 1984
Title: The Refined Structure of Ribonuclease-A at 1.45 Angstroms Resolution
Authors: Borkakoti, N. / Moss, D.S. / Stanford, M.J. / Palmer, R.A.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: Ribonuclease-A: Least-Squares Refinement of the Structure at 1.45 Angstroms Resolution
Authors: Borkakoti, N. / Moss, D.S. / Palmer, R.A.
History
DepositionJul 18, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9164
Polymers13,7081
Non-polymers1,2083
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.500, 38.700, 53.700
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 93 / 2: CIS PROLINE - PRO 114

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Components

#1: Protein RIBONUCLEASE A / RNASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CO-CRYSTALLIZED COMPLEX / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CGP / 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE


Mass: 556.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N8O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal grow
*PLUS
Method: unknown / Details: Carlisle, C. H., (1974) J. Mol. Biol., 85, 1. / PH range low: 5.7 / PH range high: 5.2
Components of the solutions
*PLUS
Conc.: 30-40 % / Common name: ethanol

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.94 Å / Num. obs: 7807 / % possible obs: 89 % / Num. measured all: 17427 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 2.12 Å / % possible obs: 76 %

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.218 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 28 58 1037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_d0.053
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.058

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