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- PDB-3zwn: Crystal structure of Aplysia cyclase complexed with substrate NGD... -

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Basic information

Entry
Database: PDB / ID: 3zwn
TitleCrystal structure of Aplysia cyclase complexed with substrate NGD and product cGDPR
ComponentsADP-RIBOSYL CYCLASECyclic ADP-ribose
KeywordsHYDROLASE
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
CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE / Chem-NGD / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKotaka, M. / Graeff, R. / Zhang, L.H. / Lee, H.C. / Hao, Q.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase.
Authors: Kotaka, M. / Graeff, R. / Chen, Z. / Zhang, L.H. / Lee, H.C. / Hao, Q.
History
DepositionAug 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6844
Polymers59,4442
Non-polymers1,2402
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-21.2 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.494, 57.852, 71.303
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8639, -0.3603, -0.352), (-0.3903, 0.0372, 0.9199), (-0.3184, 0.9321, -0.1727)
Vector: 51.1512, -4.722, 25.9524)

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Components

#1: Protein ADP-RIBOSYL CYCLASE / Cyclic ADP-ribose / ADRC / NAD GLYCOHYDROLASE / NAD(+) NUCLEOSIDASE / NADASE


Mass: 29722.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical ChemComp-CGR / CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE / CYCLIC GDP-RIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-NGD / 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM / NICOTINAMIDE GUANINE DINUCLEOTIDE


Mass: 680.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O15P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ADDITIONAL ALANINE AT THE N-TERMINUS ARE ACTUALLY AMINO ACIDS LEFT OVER FROM THE CLEAVAGE OF ...THE ADDITIONAL ALANINE AT THE N-TERMINUS ARE ACTUALLY AMINO ACIDS LEFT OVER FROM THE CLEAVAGE OF THE SECRETORY SIGNALLING PROTEIN FOR SECRETION DURING EXPRESSION FROM PICHIA.

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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: 2.84 Å3/Da / Density % sol: 56.71 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 48804 / % possible obs: 94 % / Observed criterion σ(I): 1.4 / Redundancy: 3.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.4 / % possible all: 69.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R12

1r12


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.003 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23278 2484 5.1 %RANDOM
Rwork0.17631 ---
obs0.17914 46173 94.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-1.1 Å2
2---0.38 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 81 452 4572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9865766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65323.571196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96315700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2271528
X-RAY DIFFRACTIONr_chiral_restr0.1780.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.21.52523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04924067
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.33131719
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2224.51699
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 133 -
Rwork0.262 2442 -
obs--68.27 %
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)
10.6496-0.2012-0.16290.71450.29920.3622-0.0022-0.0221-0.0230.0243-0.0053-0.0574-0.02540.02480.00740.0522-0.00590.0070.03990.01250.015939.29751.515819.7319
20.59380.18120.25340.47140.40990.5011-0.0169-0.0196-0.0468-0.04290.00050.0307-0.0315-0.01130.01640.02710.00090.00550.00530.00370.01519.6721-1.518610.9168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 251
2X-RAY DIFFRACTION1A2458
3X-RAY DIFFRACTION2B0 - 251
4X-RAY DIFFRACTION2B5573

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