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- PDB-3i9j: Crystal structure of ADP ribosyl cyclase complexed with a substra... -

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Basic information

Entry
Database: PDB / ID: 3i9j
TitleCrystal structure of ADP ribosyl cyclase complexed with a substrate analog and a product nicotinamide
ComponentsADP-ribosyl cyclase
KeywordsHYDROLASE / Homodimer / enzyme-analog-nicotinamide complex / ADP-ribosyl cyclase / Disulfide bond / Fertilization / NAD
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
Chem-AVV / NICOTINAMIDE / Nicotinamide 2-fluoro-adenine dinucleotide / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLiu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for enzymatic evolution from a dedicated ADP-ribosyl cyclase to a multifunctional NAD hydrolase
Authors: Liu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q.
History
DepositionJul 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl cyclase
B: ADP-ribosyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5255
Polymers59,1602
Non-polymers1,3653
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-4 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.121, 57.121, 364.683
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein ADP-ribosyl cyclase / ADRC / NAD(+) nucleosidase / NADase / NAD glycohydrolase


Mass: 29579.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: PPICZ(ALPHA)A / Production host: Pichia Pastoris (fungus) / Strain (production host): X-33 (INVITROGEN) / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical ChemComp-NFD / Nicotinamide 2-fluoro-adenine dinucleotide / 2-fluoro-NAD+


Mass: 681.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26FN7O14P2
#3: Chemical ChemComp-AVV / [(2R,3S,4R,5R)-5-(6-amino-2-fluoro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / 2-fluoro-adenosine diphosphate ribose, 2F-ADPRI


Mass: 561.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22FN5O13P2
#4: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M imidazole, pH 7.5, 12-24% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. all: 33025 / Num. obs: 33025 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.18→2.26 Å / % possible all: 70.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBE

1lbe


Resolution: 2.18→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.709 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.246 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24781 1644 5 %RANDOM
Rwork0.19666 ---
all0.19932 ---
obs0.19932 32751 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 101.87 Å2 / Biso mean: 49.824 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å21.43 Å20 Å2
2--2.86 Å20 Å2
3----4.29 Å2
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 90 129 4243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224235
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9865752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.97523.571196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59215700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7521528
X-RAY DIFFRACTIONr_chiral_restr0.1280.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213218
X-RAY DIFFRACTIONr_mcbond_it1.0181.52508
X-RAY DIFFRACTIONr_mcangle_it1.80824046
X-RAY DIFFRACTIONr_scbond_it3.23631727
X-RAY DIFFRACTIONr_scangle_it4.9484.51706
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 76 -
Rwork0.265 1648 -
all-1724 -
obs--68.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04180.6136-0.18820.77870.22152.9186-0.1428-0.1387-0.09730.08660.11790.0177-0.4293-0.32310.0250.15620.15140.0125-0.32610.0106-0.11932.3998.89114.485
21.49540.9888-0.04681.51260.12423.1582-0.1680.1794-0.0057-0.12680.20240.1048-0.0201-0.1174-0.0343-0.0713-0.13960.0123-0.2701-0.0084-0.08849.132-0.557-14.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 251
2X-RAY DIFFRACTION2B1 - 251

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