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- PDB-1lbe: APLYSIA ADP RIBOSYL CYCLASE -

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Basic information

Entry
Database: PDB / ID: 1lbe
TitleAPLYSIA ADP RIBOSYL CYCLASE
ComponentsADP RIBOSYL CYCLASE
KeywordsHYDROLASE / NAD(+) NUCLEOSIDASE / NADASE
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NAD+ nucleosidase activity, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / positive regulation of B cell proliferation / transferase activity / cytoplasmic vesicle / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsPrasad, G.S. / Mcree, D.E. / Stura, E.A. / Levitt, D.G. / Lee, H.C. / Stout, C.D.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of Aplysia ADP ribosyl cyclase, a homologue of the bifunctional ectozyme CD38.
Authors: Prasad, G.S. / McRee, D.E. / Stura, E.A. / Levitt, D.G. / Lee, H.C. / Stout, C.D.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of Adp-Ribosyl Cyclase from Aplysia Californica
Authors: Pradas, G.S. / Levitt, D.G. / Lee, H.C. / Stout, C.D.
History
DepositionSep 18, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP RIBOSYL CYCLASE
B: ADP RIBOSYL CYCLASE


Theoretical massNumber of molelcules
Total (without water)59,1602
Polymers59,1602
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.200, 72.300, 125.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP RIBOSYL CYCLASE / CYCLASE / NADASE


Mass: 29579.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aplysia californica (California sea hare) / Organ: OVOTESTIS / References: UniProt: P29241, NAD+ glycohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.68 Å3/Da / Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.0 OD280protein1drop
240 mM1dropNaCl
310 mMHEPES1drop
430 %(w/v)PEG40001reservoir
50.2 Mimidazole-malate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 84127 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Rmerge(I) obs: 0.103
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 25029 / Num. measured all: 84127

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 2.4→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.299 -
Rwork0.214 -
obs0.214 23824
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 0 69 4066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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