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- PDB-1r5c: X-ray structure of the complex of Bovine seminal ribonuclease swa... -

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Basic information

Entry
Database: PDB / ID: 1r5c
TitleX-ray structure of the complex of Bovine seminal ribonuclease swapping dimer with d(CpA)
ComponentsRibonuclease, seminal
KeywordsHYDROLASE / ribonucleases / protein dynamics / protein structure-function / ligand binding / population shift / 3D domain swapping
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMerlino, A. / Vitagliano, L. / Sica, F. / Zagari, A. / Mazzarella, L.
Citation
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.
#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. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A.
#2: 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.
#3: Journal: J.Cryst.Growth / Year: 1996
Title: Cosolute Effect on Crystallization of Two Dinucleotide Complexes of Bovine Seminal Ribonuclease from Concentrated Salt Solutions
Authors: Sica, F. / Adinolfi, S. / Vitagliano, L. / Zagari, A. / Capasso, S. / 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: J.Cryst.Growth / Year: 1999
Title: Crystallization of Multiple Forms of Bovine Seminal Ribonuclease: the liganded and Unliganded State
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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
Revision 1.4Oct 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: Ribonuclease, seminal
B: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3464
Polymers27,2652
Non-polymers1,0812
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-22 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.540, 60.020, 83.690
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 / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13632.640 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.: 91 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.4
Details: 62-64% saturation ammonium sulfate, 8-10% 2-methyl-2,4-pentandiol, dinucleotide-protein molar ratio of 8:1, pH 5.4, MICRO-BATCH, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Nov 10, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 13184 / Num. obs: 13184 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.279 / % possible all: 91.8

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Processing

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

1bsr


Resolution: 2.1→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 615 RANDOM
Rwork0.19 --
all0.2 12521 -
obs0.193 12054 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 74 91 2047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6

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