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- PDB-1rob: STRUCTURE OF THE CRYSTALLINE COMPLEX OF CYTIDYLIC ACID (2'-CMP) W... -

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Basic information

Entry
Database: PDB / ID: 1rob
TitleSTRUCTURE OF THE CRYSTALLINE COMPLEX OF CYTIDYLIC ACID (2'-CMP) WITH RIBONUCLEASE AT 1.6 ANGSTROMS RESOLUTION
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
CYTIDINE-2'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsLisgarten, J.N. / Palmer, R.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 A resolution. Conservation of solvent sites in RNase-A high-resolution structures.
Authors: Lisgarten, J.N. / Gupta, V. / Maes, D. / Wyns, L. / Zegers, I. / Palmer, R.A. / Dealwis, C.G. / Aguilar, C.F. / Hemmings, A.M.
#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.Mol.Biol. / Year: 1987
Title: X-Ray Refinement Study on the Binding of Cytidylic Acid (2'-Cmp) to Ribonuclease A
Authors: Howlin, B. / Harris, W. / Moss, D.S. / Palmer, R.A.
#3: 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
DepositionAug 23, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 23, 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)14,0322
Polymers13,7081
Non-polymers3231
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.512, 38.242, 53.303
Angle α, β, γ (deg.)90.00, 106.10, 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


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-C2P / CYTIDINE-2'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal grow
*PLUS
Method: unknown / 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
Num. obs: 11945 / Num. measured all: 39576
Reflection shell
*PLUS
Highest resolution: 1.54 Å / Lowest resolution: 1.63 Å / % possible obs: 76 % / Rmerge(I) obs: 0.227

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.17 / Highest resolution: 1.6 Å
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 21 101 1077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.051
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 11945 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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