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- PDB-1og1: CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP-RIBOSYLTRANSFERASE A... -

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Basic information

Entry
Database: PDB / ID: 1og1
TitleCRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP-RIBOSYLTRANSFERASE ART2.2 IN COMPLEX WITH TAD
ComponentsT-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE / IMMUNO-REGULATION
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+ glycohydrolase / NAD+-protein-arginine ADP-ribosyltransferase activity / NAD+ catabolic process / NAD+ nucleosidase activity / hydrolase activity, acting on glycosyl bonds / NAD+ poly-ADP-ribosyltransferase activity / side of membrane / nucleotidyltransferase activity / plasma membrane
Similarity search - Function
NAD:arginine ADP-ribosyltransferases signature. / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / : / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-TAD / T-cell ecto-ADP-ribosyltransferase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRitter, H. / Koch-Nolte, F. / Marquez, V.E. / Schulz, G.E.
CitationJournal: Biochemistry / Year: 2003
Title: Substrate Binding and Catalysis of Ecto-Adp-Ribosyltransferase 2.2 From Rat
Authors: Ritter, H. / Koch-Nolte, F. / Marquez, V.E. / Schulz, G.E.
History
DepositionApr 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7362
Polymers26,0681
Non-polymers6671
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.419, 81.419, 77.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2


Mass: 26068.447 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PASK60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM522
References: UniProt: P20974, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-TAD / BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE


Mass: 667.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N7O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.562 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.3
Details: 100 MM TRIS PH8.3, 200 MM LI2SO4, 22 % PEG4000, pH 8.30
Crystal grow
*PLUS
Method: other / Details: Mueller-Dieckmann., (2002) Acta Cryst., D58, 1211.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 20469 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.3
Reflection shellResolution: 2→2.02 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 4.3 % / Num. unique obs: 698 / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GY0

1gy0


Resolution: 2→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1391101.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 990 4.9 %RANDOM
Rwork0.202 ---
obs0.202 20352 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5311 Å2 / ksol: 0.401936 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å2-2.03 Å20 Å2
2---2.13 Å20 Å2
3---4.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-20 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 43 179 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.832.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 161 4.8 %
Rwork0.25 3184 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: MET1.PAR / Topol file: MET1.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.59

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