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- PDB-1gxy: crystal structure of the eucaryotic mono-ADP-ribosyltransferase A... -

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Basic information

Entry
Database: PDB / ID: 1gxy
Titlecrystal structure of the eucaryotic mono-ADP-ribosyltransferase ART2.2; CRYSTAL FORM A (P21)
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
T-cell ecto-ADP-ribosyltransferase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.71 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 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)52,3214
Polymers52,1372
Non-polymers1842
Water8,971498
1
A: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1612
Polymers26,0681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1612
Polymers26,0681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.510, 85.640, 57.960
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.12554, 0.02431, -0.99179), (-0.02801, -0.99939, -0.02095), (-0.99169, 0.02515, 0.12614)
Vector: 20.34503, 62.85789, 28.20511)

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9094
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9094 Å / Relative weight: 1
ReflectionResolution: 1.71→29 Å / Num. obs: 48705 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.034 / Net I/σ(I): 10.5
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6 / Rsym value: 0.119 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29 Å / Num. measured all: 195638 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 6787 / Rmerge(I) obs: 0.119

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.71→29 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2438 5 %RANDOM
Rwork0.187 ---
obs0.187 48658 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.77 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.42 Å2
2--1.41 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.71→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 12 498 4154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.71→1.82 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 386 4.9 %
Rwork0.219 7529 -
obs--97.9 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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