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- PDB-11ba: BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN T... -

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Basic information

Entry
Database: PDB / ID: 11ba
TitleBINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE
ComponentsPROTEIN (RIBONUCLEASE, SEMINAL)
KeywordsHYDROLASE / PHOSPHORIC DIESTER / RNA / 2'-5'-DINUCLEOTIDE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
URIDYLYL-2'-5'-PHOSPHO-ADENOSINE / : / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsVitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L.
Citation
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.
#1: Journal: J.Cryst.Growth / Year: 1997
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.
#2: 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.
#3: 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.
History
DepositionMar 17, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Aug 9, 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 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE, SEMINAL)
B: PROTEIN (RIBONUCLEASE, SEMINAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7007
Polymers27,2652
Non-polymers1,4355
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-65 kcal/mol
Surface area12840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.450, 60.640, 50.750
Angle α, β, γ (deg.)90.00, 117.35, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.724319, 0.008343, -0.689414), (-0.023453, -0.999646, 0.012543), (-0.689066, 0.025254, 0.724258)
Vector: 0.358, -0.549, -0.346)

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Components

#1: Protein PROTEIN (RIBONUCLEASE, SEMINAL)


Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COMPLEXED WITH URIDYLYL-2',5'-ADENOSINE / Source: (natural) Bos taurus (domestic cattle) / Secretion: SEMINAL FLUID / References: UniProt: P00669, GenBank: 1438988, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UPA / URIDYLYL-2'-5'-PHOSPHO-ADENOSINE


Mass: 573.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N7O12P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
162-64 %satammonium sulfate11
28-10 %(v/v)MPD11
310 mg/mlprotein11
4nucleotide/protein11molar ratio of 8:1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→10 Å / Num. obs: 15798 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.06→2.25 Å / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

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

1bsr


Resolution: 2.06→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.184 --
obs-14764 92 %
Refinement stepCycle: LAST / Resolution: 2.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 93 108 2083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.85
X-RAY DIFFRACTIONx_plane_restr0.008
X-RAY DIFFRACTIONx_chiral_restr0.117

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