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- PDB-11bg: A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BO... -

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Basic information

Entry
Database: PDB / ID: 11bg
TitleA POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE
ComponentsPROTEIN (BOVINE SEMINAL RIBONUCLEASE)
KeywordsHYDROLASE / PHOSPHORIC DIESTER / RNA
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
URIDYLYL-2'-5'-PHOSPHO-GUANOSINE / Seminal ribonuclease / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsVitagliano, L. / Adinolfi, S. / Sica, F. / Merlino, A. / Zagari, A. / Mazzarella, L.
Citation
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.
#1: Journal: J.Cryst.Growth / Year: 1999
Title: Crystallization of Multiple Forms of Bovine Seminal Ribonuclease in the Liganded and Unliganded State
Authors: Sica, F. / Adinolfi, S. / Berisio, R. / De Lorenzo, C. / Mazzarella, L. / Piccoli, R. / Vitagliano, L. / 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: 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.
#4: 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.
#5: 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 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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 6, 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: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
B: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,39114
Polymers27,2652
Non-polymers3,12612
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-140 kcal/mol
Surface area12690 Å2
MethodPISA
2
A: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
B: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
hetero molecules

A: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
B: PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,78328
Polymers54,5314
Non-polymers6,25224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_566x,-y+1,-z+11
Buried area18060 Å2
ΔGint-337 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.400, 66.700, 107.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-129-

SO4

21A-319-

HOH

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Components

#1: Protein PROTEIN (BOVINE SEMINAL RIBONUCLEASE)


Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BOVINE (BOS TAURUS) SEMINAL FLUID / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: RNS_BOVIN, UniProt: P00669*PLUS, EC: 3.1.27.5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-U2G / URIDYLYL-2'-5'-PHOSPHO-GUANOSINE / PHOSPHORIC ACID-2'-[2'-DEOXY-URIDINE]ESTER-5'-GUANOSINE ESTER


Mass: 589.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H24N7O13P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown / Details: nucleotide to protein molar ratio of 8:1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
162-64 %satammonium sulfate11
28-10 %(v/v)MPD11
310 mg/mlprotein11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 20713 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.9→1.93 Å / % possible all: 90.3
Reflection
*PLUS
Num. measured all: 97315
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1BSR

1bsr


Resolution: 1.9→12 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.189 --
obs-19644 92.1 %
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 157 124 2163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 3 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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