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- PDB-1tq9: Non-covalent swapped dimer of Bovine Seminal Ribonuclease in comp... -

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Basic information

Entry
Database: PDB / ID: 1tq9
TitleNon-covalent swapped dimer of Bovine Seminal Ribonuclease in complex with 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE
ComponentsRibonuclease, seminal
KeywordsHYDROLASE / Protein-dinucleotide complex / Cytotoxic action
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 / identical protein binding
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-CPA / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSica, F. / Di Fiore, A. / Merlino, A. / Mazzarella, L.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Bovine seminal ribonuclease: structure at 1.9 A resolution
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Dilorenzo, G. / Mattia, C.A. / Zagari, A.
#2: Journal: Biopolymers / Year: 2004
Title: Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer
Authors: Merlino, A. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L.
#3: Journal: Protein Sci. / Year: 1998
Title: Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine
Authors: Vitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L.
#4: 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.
#5: Journal: Proteins / Year: 2003
Title: The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative
Authors: Sica, F. / Di Fiore, A. / Zagari, A. / Mazzarella, L.
#6: Journal: FEBS Lett. / Year: 2003
Title: Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease
Authors: Berisio, R. / Sica, F. / De Lorenzo, C. / Di Fiore, A. / Piccoli, R. / Zagari, A. / Mazzarella, L.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22
Authors: Mazzarella, L. / Vitagliano, L. / Zagari, A.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease, seminal
B: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5744
Polymers27,4932
Non-polymers1,0812
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-17 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.471, 69.689, 110.804
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, seminal / pancreatic type ribonuclease / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13746.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-CPA / 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE


Mass: 540.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N8O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, isopropanol, sodium acetate, cacodilate, 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 12, 2000
RadiationMonochromator: syncrothron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 21846 / Num. obs: 21846 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.84 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34
Reflection shellResolution: 2→2.03 Å / Redundancy: 8 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 7 / Num. unique all: 1059 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BSR

1bsr


Resolution: 2→10 Å / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2062 -RANDOM
Rwork0.206 ---
all0.212 20868 --
obs0.212 18806 92.8 %-
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 74 121 2093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_improper_angle_d1

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