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- PDB-1rnd: NEWLY OBSERVED BINDING MODE IN PANCREATIC RIBONUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1rnd
TitleNEWLY OBSERVED BINDING MODE IN PANCREATIC RIBONUCLEASE
ComponentsRIBONUCLEASE A
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
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsAguilar, C.F. / Thomas, P.J. / Mills, A. / Moss, D.S. / Palmer, R.A.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Newly observed binding mode in pancreatic ribonuclease.
Authors: Aguilar, C.F. / Thomas, P.J. / Mills, A. / Moss, D.S. / Palmer, R.A.
#1: Journal: Biochim.Biophys.Acta / Year: 1991
Title: Novel Non-Productively Bound Ribonuclease Inhibitor Complexes-High Resolution X-Ray Refinement Studies on the Binding of Rnase-A to Cytidylyl-2',5'-Guanosine (2',5'Cpg) and Deoxycytidylyl- ...Title: Novel Non-Productively Bound Ribonuclease Inhibitor Complexes-High Resolution X-Ray Refinement Studies on the Binding of Rnase-A to Cytidylyl-2',5'-Guanosine (2',5'Cpg) and Deoxycytidylyl-3',5'-Guanosine (3',5'Dcpdg)
Authors: Aguilar, C.F. / Thomas, P.J. / Moss, D.S. / Mills, A. / Palmer, R.A.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: X-Ray Refinement Study on the Binding of Cytidylic Acid (2'-Cmp) to Ribonuclease-A
Authors: Howlin, B. / Harris, G.W. / Moss, D.S. / Palmer, R.A.
#3: Journal: Biochim.Biophys.Acta / Year: 1984
Title: An X-Ray Refinement Study on the Binding of Ribonuclease-A to Cytidine-N(3)-Oxide 2'-Phosphate
Authors: Palmer, R.A. / Moss, D.S. / Haneef, I. / Borkakoti, N.
#4: 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.
History
DepositionOct 21, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1523
Polymers13,7081
Non-polymers4432
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.340, 38.190, 53.370
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO 93 AND PRO 114 ARE CIS PROLINES.

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MOST INTERESTING FEATURE IN THIS STRUCTURE IS THE MODE OF BINDING OF THE DCPDG INHIBITOR TO THE ...THE MOST INTERESTING FEATURE IN THIS STRUCTURE IS THE MODE OF BINDING OF THE DCPDG INHIBITOR TO THE ENZYME. THE ACTIVE SITE OF THE ENZYME WAS LABELLED B1, P1, B2 (FOLLOWING F.M.RICHARDS AND H.W.WYCKOFF (1973) IN "ATLAS OF MOLECULAR STRUCTURES IN BIOLOGY - I: RIBONUCLEASE-S" D.C. PHILLIPS AND F.M.RICHARDS (EDS.) CLARENDON, OXFORD) WHERE P1 IS THE SITE AT WHICH THE PHOSPHODIESTER BOND IS CLEAVED AND IS OCCUPIED BY THE INORGANIC PHOSPHATE (OR SULFATE) IN THE NATIVE STRUCTURE. B1 IS THE SITE AT WHICH BASE IDENTIFICATION IS MADE THROUGH THR 45, BEING A SPECIFIC BINDING PLACE FOR PYRIMIDINE BASES. B2 IS THE SECOND BINDING PLACE FOR EITHER PURINE OR PYRIMIDINES. IN THIS STRUCTURE THE GUANINE BASE OF DCPDG BINDS TO THR 45 IN THE B1 SITE AND THE PHOSPHATE/SULFATE IN P1 (WHICH IS NOT DISPLACED BY THE INHIBITOR), WITH THE CPG MOLECULE PROTRUDING 'BACKWARDS' AWAY FROM THE ACTIVE SITE TOWARD THE OUTSIDE OF THE RIBONUCLEASE MOLECULAR SURFACE.
Has protein modificationY
Nonpolymer detailsTHE ATOMIC COORDINATES FOR THE DEOXYCYTIDINE PART OF DCPDG ARE NOT INCLUDED IN THIS DATA SET ...THE ATOMIC COORDINATES FOR THE DEOXYCYTIDINE PART OF DCPDG ARE NOT INCLUDED IN THIS DATA SET BECAUSE THE ELECTRON DENSITY FOR THIS PART OF THE MOLECULE WAS NOT WELL DEFINED DUE TO LACK OF INTERACTIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal grow
*PLUS
Method: unknown / PH range low: 5.7 / PH range high: 5.2
Components of the solutions
*PLUS
Conc.: 47 %(v/v) / Common name: ethanol

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementHighest resolution: 1.5 Å
Details: THE INHIBITOR AND SULFATE ANION WERE REFINED USING GROUP OCCUPANCIES.
RfactorNum. reflection
obs0.19 16347
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 28 96 1058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_deg1.22
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Num. reflection all: 16347 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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