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- PDB-6y75: BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A) -

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Basic information

Entry
Database: PDB / ID: 6y75
TitleBIL2 domain from T.thermophila BUBL1 locus (C1A-N143A)
Components(NAD(P)(+)--arginine ADP- ...) x 2
KeywordsSPLICING / intein / PTM / ubiquitin
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / intein-mediated protein splicing / nucleotidyltransferase activity / modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region ...Vint domain / Hint-domain / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / NAD(P)(+)--arginine ADP-ribosyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIlari, A. / Chiarini, V.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationPRIN20154JRJPP Italy
Citation
Journal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya.
Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A.
#1: Journal: Biochim.Biophys.Acta / Year: 2021
Title: Structural basis of ubiquitination mediated by protein splicing in early Eukarya
Authors: Chiarini, V. / Fiorillo, A. / Camerini, S. / Crescenzi, M. / Nakamura, S. / Battista, T. / Guidoni, L. / Colotti, G. / Ilari, A.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)(+)--arginine ADP-ribosyltransferase
B: NAD(P)(+)--arginine ADP-ribosyltransferase
C: NAD(P)(+)--arginine ADP-ribosyltransferase
D: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97812
Polymers69,4124
Non-polymers5668
Water4,828268
1
A: NAD(P)(+)--arginine ADP-ribosyltransferase
B: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1418
Polymers34,7062
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NAD(P)(+)--arginine ADP-ribosyltransferase
D: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8374
Polymers34,7062
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.821, 67.605, 82.445
Angle α, β, γ (deg.)90.000, 114.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A78 - 230
2114B78 - 230
3114C78 - 230
4114D78 - 230

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.197352, -0.968334, -0.152911), (-0.969996, 0.17029, 0.173517), (-0.141983, 0.182567, -0.972887)-8.75422, -21.03252, 89.479698
3given(-0.028602, 0.990995, -0.130806), (-0.988579, -0.047414, -0.143052), (-0.147965, 0.125221, 0.981033)0.15792, 3.27812, -50.942791
4given(0.986437, -0.161483, 0.029403), (-0.162964, -0.942149, 0.292913), (-0.019599, -0.293732, -0.955687)-5.62386, -31.33918, 139.14238

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Components

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NAD(P)(+)--arginine ADP- ... , 2 types, 4 molecules ACBD

#1: Protein NAD(P)(+)--arginine ADP-ribosyltransferase / Mono(ADP-ribosyl)transferase


Mass: 17502.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase
#2: Protein NAD(P)(+)--arginine ADP-ribosyltransferase / Mono(ADP-ribosyl)transferase


Mass: 17203.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Gene: TTHERM_00085190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q236S9, NAD+-protein-arginine ADP-ribosyltransferase

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Non-polymers , 4 types, 276 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: Mg formate 0.1M, PEG3350 19%, Tris 50mM, NaCl 250 mM.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34430 / % possible obs: 99.1 % / Redundancy: 3.36 % / Biso Wilson estimate: 40.902 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.15 / Net I/σ(I): 7.23
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.41 % / Num. unique obs: 10795 / CC1/2: 0.83 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TMM

6tmm


Resolution: 2.3→47.57 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.649 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3018 1662 4.8 %RANDOM
Rwork0.2538 ---
obs0.256 32698 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 34.514 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.05 Å2
2---0.12 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.3→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 24 268 5178
Biso mean--55.41 32.64 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125018
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.636769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46124.776268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10715885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9891512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023800
Refine LS restraints NCS

Ens-ID: 1 / Number: 1211 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.210.5
2BMEDIUM POSITIONAL0.230.5
3CMEDIUM POSITIONAL0.250.5
4DMEDIUM POSITIONAL0.280.5
1AMEDIUM THERMAL4.942
2BMEDIUM THERMAL4.842
3CMEDIUM THERMAL4.032
4DMEDIUM THERMAL9.22
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.378 133 -
Rwork0.338 2384 -
obs--99.21 %

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