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- PDB-1y92: Crystal structure of the P19A/N67D Variant Of Bovine seminal Ribo... -

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Basic information

Entry
Database: PDB / ID: 1y92
TitleCrystal structure of the P19A/N67D Variant Of Bovine seminal Ribonuclease
ComponentsSeminal ribonuclease
KeywordsHYDROLASE / nuclease
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
Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPicone, D. / Di Fiore, A. / Ercole, C. / Franzese, M. / Sica, F. / Tomaselli, S. / Mazzarella, L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: The Role of the Hinge Loop in Domain Swapping: THE SPECIAL CASE OF BOVINE SEMINAL RIBONUCLEASE.
Authors: Picone, D. / Di Fiore, A. / Ercole, C. / Franzese, M. / Sica, F. / Tomaselli, S. / Mazzarella, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Bovine seminal ribonuclease: structure at 1.9 resolution
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, 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: 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.
#4: 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.
#5: 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.
#6: 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.
#7: Journal: J.Mol.Biol. / Year: 1999
Title: A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.
History
DepositionDec 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: Seminal ribonuclease
B: Seminal ribonuclease


Theoretical massNumber of molelcules
Total (without water)27,2152
Polymers27,2152
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-20 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.500, 62.433, 81.594
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 Seminal ribonuclease / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13607.587 Da / Num. of mol.: 2 / Mutation: P19A, N67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: SRN / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P00669, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, Tris-HCl, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Dec 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 12492 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / Num. unique all: 681 / % possible all: 93.5

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Processing

Software
NameClassification
ENRAF-NONIUSdata collection
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R5D

1r5d


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.202 1150 RANDOM
Rwork0.171 --
all0.209 11167 -
obs0.191 10017 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 96 1949

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