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

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Basic information

Entry
Database: PDB / ID: 6tmm
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 / metal ion binding
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 SB210 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.398 Å
AuthorsChiarini, V. / Ilari, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationPRIN 20154JRJPP 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
DepositionDec 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: NAD(P)(+)--arginine ADP-ribosyltransferase
BBB: NAD(P)(+)--arginine ADP-ribosyltransferase
CCC: NAD(P)(+)--arginine ADP-ribosyltransferase
DDD: NAD(P)(+)--arginine ADP-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,59821
Polymers71,1434
Non-polymers1,45517
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-156 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.477, 72.769, 70.264
Angle α, β, γ (deg.)90.000, 97.871, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-807-

CA

Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB CCC DDD)

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Components

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

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


Mass: 17842.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila 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: 17729.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila 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 , 5 types, 140 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: Mg formate 0.1 M, PEG3350 19%, Tris 50 mM, 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: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.398→69.602 Å / Num. obs: 26317 / % possible obs: 98.9 % / Redundancy: 3.36 % / Biso Wilson estimate: 58.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.071 / Net I/σ(I): 12.25
Reflection shellResolution: 2.398→2.54 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 8236 / CC1/2: 0.733 / Rrim(I) all: 0.704 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.398→69.602 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.873 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.298
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2665 1333 5.096 %
Rwork0.1976 --
all0.201 --
obs-26159 99.403 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.817 Å2
Baniso -1Baniso -2Baniso -3
1--1.732 Å2-0 Å2-0.362 Å2
2--3.26 Å20 Å2
3----1.376 Å2
Refinement stepCycle: LAST / Resolution: 2.398→69.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 45 123 5177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174669
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.6366985
X-RAY DIFFRACTIONr_angle_other_deg1.1051.57410903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3715626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95124.834271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46215916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4591512
X-RAY DIFFRACTIONr_chiral_restr0.0470.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.1890.2916
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24504
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22323
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.22319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2167
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1660.23
X-RAY DIFFRACTIONr_metal_ion_refined0.4480.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.219
X-RAY DIFFRACTIONr_nbd_other0.1870.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.25
X-RAY DIFFRACTIONr_mcbond_it2.8465.9762501
X-RAY DIFFRACTIONr_mcbond_other2.8465.9782502
X-RAY DIFFRACTIONr_mcangle_it4.5848.9523125
X-RAY DIFFRACTIONr_mcangle_other4.5838.9533126
X-RAY DIFFRACTIONr_scbond_it2.8716.3652677
X-RAY DIFFRACTIONr_scbond_other2.8716.3592671
X-RAY DIFFRACTIONr_scangle_it4.8029.3753859
X-RAY DIFFRACTIONr_scangle_other4.8029.3763860
X-RAY DIFFRACTIONr_lrange_it7.76668.6335356
X-RAY DIFFRACTIONr_lrange_other7.74168.615347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.398-2.460.4271090.3461794X-RAY DIFFRACTION98.2447
2.46-2.5280.3691030.3031775X-RAY DIFFRACTION99.7345
2.528-2.6010.335870.2821756X-RAY DIFFRACTION99.8916
2.601-2.6810.319900.2781661X-RAY DIFFRACTION99.4886
2.681-2.7690.363900.2731624X-RAY DIFFRACTION99.8834
2.769-2.8660.309790.2561585X-RAY DIFFRACTION100
2.866-2.9740.389940.2481521X-RAY DIFFRACTION100
2.974-3.0950.276880.241460X-RAY DIFFRACTION99.871
3.095-3.2320.356800.2311433X-RAY DIFFRACTION99.934
3.232-3.390.267590.2251350X-RAY DIFFRACTION99.8583
3.39-3.5720.303890.2211255X-RAY DIFFRACTION98.8962
3.572-3.7890.258630.1971218X-RAY DIFFRACTION99.2254
3.789-4.0490.212580.1821156X-RAY DIFFRACTION99.0212
4.049-4.3720.226610.1511041X-RAY DIFFRACTION99.6383
4.372-4.7880.175460.1271000X-RAY DIFFRACTION99.4297
4.788-5.350.178460.144895X-RAY DIFFRACTION99.6822
5.35-6.1710.293320.185795X-RAY DIFFRACTION98.9234
6.171-7.5440.237320.184672X-RAY DIFFRACTION98.1869
7.544-10.6060.173200.147522X-RAY DIFFRACTION97.307
10.606-69.6020.4770.196313X-RAY DIFFRACTION96.3855

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