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- PDB-1og3: Crystal structure of the eukaryotic mono-ADP-ribosyltransferase A... -

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Basic information

Entry
Database: PDB / ID: 1og3
TitleCrystal structure of the eukaryotic mono-ADP-ribosyltransferase ART2.2 mutant E189I in complex with NAD
ComponentsT-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE / IMMUNO-REGULATION
Function / homology
Function and homology information


NAD+ glycohydrolase / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / NAD catabolic process / NAD+ nucleosidase activity / hydrolase activity, acting on glycosyl bonds / NAD+ nucleotidase, cyclic ADP-ribose generating / NAD+-protein 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / T-cell ecto-ADP-ribosyltransferase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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 24, 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 1.4Dec 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
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)26,7162
Polymers26,0521
Non-polymers6631
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.707, 81.707, 77.810
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: 26052.492 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-246 / Mutation: YES
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION RESIDUE GLU (209) ILE
Sequence detailsMUTANT E189I

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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: 2.599 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.3
Details: 100 MM TRIS PH8.3, 200 MM LI2SO4, 22 % PEG4000, pH 8.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 9591 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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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: 2.6→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1152205.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 773 8.1 %RANDOM
Rwork0.2 ---
obs0.2 9543 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.346 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å22.87 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-20 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 44 154 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 123 8 %
Rwork0.219 1424 -
obs--100 %
Xplor fileSerial no: 1 / Param file: NADNEU.PAR / Topol file: NADNEU.TOP

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