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- PDB-1r15: Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P -

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Basic information

Entry
Database: PDB / ID: 1r15
TitleAplysia ADP ribosyl cyclase with bound nicotinamide 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 / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / transferase activity / cytoplasmic vesicle / 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 / NICOTINAMIDE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
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
C: ADP-ribosyl cyclase
D: ADP-ribosyl cyclase
E: ADP-ribosyl cyclase
F: ADP-ribosyl cyclase
G: ADP-ribosyl cyclase
H: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,30632
Polymers236,6408
Non-polymers3,66724
Water0
1
A: ADP-ribosyl cyclase
B: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0778
Polymers59,1602
Non-polymers9176
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint11 kcal/mol
Surface area22410 Å2
MethodPISA
2
C: ADP-ribosyl cyclase
D: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0778
Polymers59,1602
Non-polymers9176
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint13 kcal/mol
Surface area22370 Å2
MethodPISA
3
E: ADP-ribosyl cyclase
F: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0778
Polymers59,1602
Non-polymers9176
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint12 kcal/mol
Surface area22380 Å2
MethodPISA
4
G: ADP-ribosyl cyclase
H: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0778
Polymers59,1602
Non-polymers9176
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint12 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 75.320, 138.130
Angle α, β, γ (deg.)88.16, 89.22, 89.09
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 29579.945 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C5H11O7P
#3: Chemical
ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 16 / Fragment: nicotinamide / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM

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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: 2.65 Å3/Da / Density % sol: 53.63 %
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, hanging drop / Details: Munshi, C., (1999) J. Biol. Chem., 274, 30770.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 %(w/v)PEG40001reservoir
20.1 Mimidazole1reservoirpH7.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.919 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.4→33 Å / Num. all: 64996 / Num. obs: 57197 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.108
Reflection
*PLUS
Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 44.7 % / Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→33 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 2859 random
Rwork0.244 --
all0.245 57197 -
obs0.245 54338 -
Refinement stepCycle: LAST / Resolution: 2.4→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16096 0 248 0 16344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0139
X-RAY DIFFRACTIONc_angle_deg1.6915
Refinement
*PLUS
Num. reflection obs: 57197 / Rfactor Rfree: 0.2694 / Rfactor Rwork: 0.2439
Solvent computation
*PLUS
Displacement parameters
*PLUS

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