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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
DescriptorRIBONUCLEASE, SEMINAL
KeywordsHYDROLASE / PHOSPHORIC DIESTER / RNA / 2'-5'-DINUCLEOTIDE
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (2.06 Å resolution / Molecular replacement)
AuthorsVitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L.
CitationProtein Sci., 1998, 7, 1691-1699

primary. Protein Sci., 1998, 7, 1691-1699 Yorodumi Papers
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.
Vitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L.

#1. J.Cryst.Growth, 1997, 168, 192-
Cosolute Effect on Crystallization of Two Dinucleotide Complexes of Bovine Seminal Ribonuclease from Concentrated Salt Solutions
Sica, F. / Adinolfi, S. / Vitagliano, L. / Zagari, A. / Capasso, S. / Mazzarella, L.

#2. Proc.Natl.Acad.Sci.USA, 1995, 92, 3799-
Swapping Structural Determinants of Ribonucleases:An Energeticanalysis of the Hinge Peptide 16-22
Mazzarella, L. / Vitagliano, L. / Zagari, A.

#3. Acta Crystallogr.,Sect.D, 1993, 49, 389-
Bovine Seminal Ribonuclease:Structure at 1.9 Angstroms Resolution
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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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: Polypeptide(L)PROTEIN (RIBONUCLEASE, SEMINAL)


Mass: 13632.640 Da / Num. of mol.: 2 / Details: COMPLEXED WITH URIDYLYL-2',5'-ADENOSINE / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P00669, GenBank: 1438988, EC: 3.1.27.5

Cellular component

Molecular function

Biological process

#2: ChemicalChemComp-SO4 / SULFATE ION


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


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


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

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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 K / Temp unit: ℃ / Method: Batch method
Crystal grow comp
*PLUS

Crystal ID: 1 / Sol ID: 1

IDConcConc unitCommon nameDetails
162-64%satammonium sulfate
28-10%(v/v)MPD
310mg/mlprotein
4nucleotide/proteinmolar 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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