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- PDB-1eow: CRYSTAL STRUCTURE OF RIBONUCLEASE A COMPLEXED WITH URIDYLYL(2',5'... -

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Basic information

Entry
Database: PDB / ID: 1eow
TitleCRYSTAL STRUCTURE OF RIBONUCLEASE A COMPLEXED WITH URIDYLYL(2',5')GUANOSINE (NON-PRODUCTIVE BINDING)
ComponentsRIBONUCLEASE PANCREATIC
KeywordsHYDROLASE / NON-PRODUCTIVE BINDING / PROTEIN-NUCLEOTIDE INTERACTIONS
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
URIDYLYL-2'-5'-PHOSPHO-GUANOSINE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsVitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L.
Citation
Journal: Protein Sci. / Year: 2000
Title: Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
Authors: Vitagliano, L. / Merlino, A. / Zagari, A. / Mazzarella, L.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: A Potential Allosteric Subsite Generated by Domain Swapping in Bovine Seminal Ribonuclease
Authors: Vitagliano, L. / Adinolfi, S. / Sica, F. / Merlino, A. / Zagari, A. / Mazzarella, L.
History
DepositionMar 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: RIBONUCLEASE PANCREATIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3943
Polymers13,7081
Non-polymers6852
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.340, 38.350, 53.850
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEASE PANCREATIC


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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-U2G / URIDYLYL-2'-5'-PHOSPHO-GUANOSINE / PHOSPHORIC ACID-2'-[2'-DEOXY-URIDINE]ESTER-5'-GUANOSINE ESTER


Mass: 589.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N7O13P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 298 K / Method: free interface diffusion / pH: 5.5
Details: 2-METHYL-2-PROPANOL, pH 5.5, FREE INTERFACE DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.3 / Details: Berisio, R., (1999) J. Mol. Biol., 292, 845.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
250 %2-methyl-2-propanol12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Apr 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 10866 / Num. obs: 10866 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.112 / Num. unique all: 1011 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 60998

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.187 -
obs0.187 10305
all-10708
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 25 72 1048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_dihedral_angle_d24
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.259 1216 -
obs--90 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
LS refinement shell
*PLUS
Rfactor Rwork: 0.259

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