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- PDB-3fl0: X-ray structure of the non covalent swapped form of the Q28L/K31C... -

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Basic information

Entry
Database: PDB / ID: 3fl0
TitleX-ray structure of the non covalent swapped form of the Q28L/K31C/S32C mutant of bovine pancreatic ribonuclease in complex with 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / 3D-domain swapping / bovine seminal ribonuclease / non-covalent dimer / antitumor activity / quaternary structure flexibility / protein mutations and evolution / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted
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 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMerlino, A. / Russo Krauss, I. / Perillo, M. / Mattia, C.A. / Ercole, C. / Picone, D. / Vergara, A. / Sica, F.
Citation
Journal: Biopolymers / Year: 2009
Title: Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants
Authors: Merlino, A. / Russo Krauss, I. / Perillo, M. / Mattia, C.A. / Ercole, C. / Picone, D. / Vergara, A. / 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: Protein Sci. / Year: 1995
Title: Hints on the evolutionary design of a dimeric RNase with special bioactions
Authors: Di Donato, A. / Cafaro, V. / Romeo, I. / D'Alessio, G.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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)28,1513
Polymers27,5952
Non-polymers5561
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-12 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.090, 62.350, 56.640
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease pancreatic / ribonuclease / RNase 1 / RNase A


Mass: 13797.485 Da / Num. of mol.: 2 / Mutation: Q28L, K31C, S32C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CGP / 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE


Mass: 556.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N8O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 35000, 0.2M sodium acetate, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 13, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 19072 / Num. obs: 19072 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KF3

1kf3


Resolution: 1.94→28.4 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 1803 RANDOM
Rwork0.174 --
all0.188 18756 -
obs0.181 18262 -
Refinement stepCycle: LAST / Resolution: 1.94→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 20 228 2163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.04

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