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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 / homologyPancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / RNA phosphodiester bond hydrolysis / pancreatic ribonuclease / ribonuclease A activity / ribonuclease activity ...Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / RNA phosphodiester bond hydrolysis / pancreatic ribonuclease / ribonuclease A activity / ribonuclease activity / nucleic acid binding / endonuclease activity / extracellular region / identical protein binding / Seminal ribonuclease / gb:1438988:
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.06 Å resolution
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 Energeticanalysis 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 Angstroms Resolution
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, L. / Mattia, C.A. / Zagari, A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 17, 1999 / Release: Mar 26, 1999
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 26, 1999Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware_software.name

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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
Polyers27,2652
Non-polymers1,4355
Water1,946108
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6120
ΔGint (kcal/M)-65
Surface area (Å2)12840
MethodPISA,PQS
Unit cell
γ
α
β
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-MP 1 21 1

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Components

#1: Protein/peptide PROTEIN (RIBONUCLEASE, SEMINAL)


Mass: 13632.640 Da / Num. of mol.: 2 / Details: COMPLEXED WITH URIDYLYL-2',5'-ADENOSINE / Source: (natural) Bos taurus (cattle) / Genus: Bos / Secretion: SEMINAL FLUID
References: UniProt: P00669, GenBank: 1438988, pancreatic ribonuclease
#2: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 108 / Formula: H2O / Water

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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 / Density percent sol: 50.36 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Temp: 20 ℃ / Method: batch method
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Details: MIRRORS / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.06 Å / D resolution low: 10 Å / Number obs: 15798 / Observed criterion sigma I: 2 / Rmerge I obs: 0.059 / Redundancy: 3 % / Percent possible obs: 92
Reflection shellHighest resolution: 2.06 Å / Lowest resolution: 2.25 Å / Percent possible all: 91
Reflection shell
*PLUS
Percent possible obs: 91

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
X-PLORmodel building
X-PLOR3.1refinement
bioteXdata scaling
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BSR
Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Sigma F: 2
Least-squares processR factor R work: 0.184 / Highest resolution: 2.06 Å / Lowest resolution: 10 Å / Number reflection obs: 14764 / Percent reflection obs: 92
Refine hist #LASTHighest resolution: 2.06 Å / Lowest resolution: 10 Å
Number of atoms included #LASTProtein: 1882 / Nucleic acid: 0 / Ligand: 93 / Solvent: 108 / Total: 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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