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- PDB-1gxz: crystal structure of the eukaryotic mono-ADP-ribosyltransferase A... -

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Basic information

Entry
Database: PDB / ID: 1gxz
Titlecrystal structure of the eukaryotic mono-ADP-ribosyltransferase ART2.2; Crystal form B (P212121)
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
5-BROMONICOTINAMIDE / T-cell ecto-ADP-ribosyltransferase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMueller-Dieckmann, C. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of the Ecto-Adp-Ribosyl Transferase Art2.2 From Rat
Authors: Mueller-Dieckmann, C. / Ritter, H. / Haag, F. / Koch-Nolte, F. / Schulz, G.E.
History
DepositionApr 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,5394
Polymers52,1372
Non-polymers4022
Water7,098394
1
A: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2692
Polymers26,0681
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2692
Polymers26,0681
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.560, 77.280, 86.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99933, 0.01574, 0.03303), (0.01717, 0.99891, 0.04344), (-0.03231, 0.04398, -0.99851)
Vector: 34.35844, 6.8794, 42.48557)

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Components

#1: Protein T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2 / ADP-RIBOSYLTRANSFERASE / T-CELL NAD(P)(+)--ARGININE ADP-RIBOSYLTRANSFERASE 2 / T-CELL MONO(ADP- ...ADP-RIBOSYLTRANSFERASE / T-CELL NAD(P)(+)--ARGININE ADP-RIBOSYLTRANSFERASE 2 / T-CELL MONO(ADP-RIBOSYL)TRANSFERASE 2 / ALLOANTIGEN RT6.2 / T-CELL SURFACE PROTEIN RT6.2


Mass: 26068.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM522
References: UniProt: P20974, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-BRT / 5-BROMONICOTINAMIDE


Mass: 201.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5BrN2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.3
Details: 100 MM TRIS PH8.3, 200 MM LI2SO4, 22 % PEG4000, pH 8.30
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Mueller-Dieckmann, C., (2002) Acta Crystallogr., D58, 1211.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.8 mg/mlprotein1drop
2100 mMTris-HCl1reservoirpH8.3
3200 mM1reservoirLi2SO4
422 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→33 Å / Num. obs: 30925 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 8.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.1
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.177 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 33 Å / Num. measured all: 126778 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 4218 / Rmerge(I) obs: 0.18

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1409 5.1 %RANDOM
Rwork0.181 ---
obs0.181 27842 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.19 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2---0.24 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 20 394 4058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it3.42
X-RAY DIFFRACTIONc_scangle_it4.742.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 242 5.3 %
Rwork0.178 4313 -
obs--100 %
Refinement
*PLUS
Lowest resolution: 33 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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