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- PDB-1r16: Aplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P -

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Basic information

Entry
Database: PDB / ID: 1r16
TitleAplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P
ComponentsADP-ribosyl cyclase
KeywordsHYDROLASE / ADP-ribosyl cyclase / cyclic ADP-ribose / NAADP / Ca2+ signalling
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
ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 3-PYRIDINYLCARBINOL / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLove, M.L. / Szebenyi, D.M.E. / Kriksunov, I.A. / Thiel, D.J. / Munshi, C. / Graeff, R. / Lee, H.C. / Hao, Q.
CitationJournal: Structure / Year: 2004
Title: ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate.
Authors: Love, M.L. / Szebenyi, D.M. / Kriksunov, I.A. / Thiel, D.J. / Munshi, C. / Graeff, R. / Lee, H.C. / Hao, Q.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE R5P UNDERGOES REACTION WITH THE PROTEIN TO FORM A 1-DEOXY INTERMEDIATE, LABELLED N, 1- ...HETEROGEN THE R5P UNDERGOES REACTION WITH THE PROTEIN TO FORM A 1-DEOXY INTERMEDIATE, LABELLED N, 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE. THE N IS COVALENTLY BOUND TO THE PROTEIN.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8066
Polymers59,1602
Non-polymers6464
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint5 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.293, 58.349, 72.368
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADP-ribosyl cyclase / NAD+ / nucleosidase / NADASE / NAD glycohydrolase / ADRC


Mass: 29579.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Escherichia coli (E. coli) / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical ChemComp-N / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 214.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O7P
#3: Chemical ChemComp-PYF / 3-PYRIDINYLCARBINOL / PYRIDIN-3-YLMETHANOL


Mass: 109.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Imidazole and 12-24 % PEG 4K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 316K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mimidazole1reservoirpH7.5
212-24 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→24 Å / Num. all: 39138 / Num. obs: 38943 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.09
Reflection
*PLUS
Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 1947 random
Rwork0.212 --
all0.214 38943 -
obs0.214 36996 -
Refinement stepCycle: LAST / Resolution: 2→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 42 92 4158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0179
X-RAY DIFFRACTIONc_angle_deg1.8143
Refinement
*PLUS
Num. reflection obs: 38943 / Rfactor Rfree: 0.2518 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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