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- PDB-3f8g: The X-ray structure of a dimeric variant of human pancreatic ribo... -

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Basic information

Entry
Database: PDB / ID: 3f8g
TitleThe X-ray structure of a dimeric variant of human pancreatic ribonuclease with high cytotoxic and antitumor activities
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / antitumor agent / ribonuclease / 3d domain swapping / unswapped dimer / dimers / Endonuclease / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMerlino, A. / Avella, G. / Mazzarella, L. / Sica, F.
Citation
Journal: Protein Sci. / Year: 2009
Title: Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
Authors: Merlino, A. / Avella, G. / Di Gaetano, S. / Arciello, A. / Piccoli, R. / Mazzarella, L. / Sica, F.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor.
Authors: Sica, F. / Di Fiore, A. / Merlino, A. / Mazzarella, L.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme.
Authors: Merlino, A. / Ercole, C. / Picone, D. / Pizzo, E. / Mazzarella, L. / Sica, F.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A dimeric mutant of human pancreatic ribonuclease with selective cytotoxicity toward malignant cells.
Authors: Piccoli, R. / Di Gaetano, S. / De Lorenzo, C. / Grauso, M. / Monaco, C. / Spalletti-Cernia, D. / Laccetti, P. / Cinatl, J. / Matousek, J. / D'Alessio, G.
#4: Journal: Biochem.J. / Year: 2001
Title: Second generation antitumour human RNase: significance of its structural and functional features for the mechanism of antitumour action.
Authors: Di Gaetano, S. / D'alessio, G. / Piccoli, R.
History
DepositionNov 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7087
Polymers28,2282
Non-polymers4805
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-74 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.855, 78.256, 80.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A / RNase UpI-1 / RIB-1 / HP-RNase


Mass: 14114.071 Da / Num. of mol.: 2 / Mutation: Q28L, R31C, R32C, N34K, E111G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE1, RIB1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07998, EC: 3.1.27.5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: A protein solution of 10mg/ml in 10mM Tris acteate ph 7.0, 300mM NaCl was equilibrated against a solution containing 27% w/v PEG, 0.2 M AS, and 100mM cacodylate buffer ph 6.5, VAPOR ...Details: A protein solution of 10mg/ml in 10mM Tris acteate ph 7.0, 300mM NaCl was equilibrated against a solution containing 27% w/v PEG, 0.2 M AS, and 100mM cacodylate buffer ph 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 9128 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E21, the crystal structure of des(1-7)RNase

1e21


Resolution: 2.6→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 462 -RANDOM
Rwork0.215 ---
all-8980 --
obs-8539 90.9 %-
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 25 162 2141

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