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- PDB-3zwv: Crystal structure of ADP-ribosyl cyclase complexed with ara-2'F-A... -

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Basic information

Entry
Database: PDB / ID: 3zwv
TitleCrystal structure of ADP-ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.3 angstrom
ComponentsADP-RIBOSYL CYCLASECyclic ADP-ribose
KeywordsHYDROLASE / CD38
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
Chem-AVU / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Jan 25, 2012Group: Other
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / reflns
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _reflns.d_resolution_high
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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)242,13916
Polymers237,7778
Non-polymers4,3628
Water5,296294
1
A: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-10.4 kcal/mol
Surface area23550 Å2
MethodPISA
2
C: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-9.5 kcal/mol
Surface area23460 Å2
MethodPISA
3
E: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-6.2 kcal/mol
Surface area23440 Å2
MethodPISA
4
G: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-7.9 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.146, 76.481, 141.366
Angle α, β, γ (deg.)88.09, 90.88, 91.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU5AA6 - 248 - 26
21GLUGLULEULEU5BB6 - 248 - 26
31GLUGLULEULEU5CC6 - 248 - 26
41GLUGLULEULEU5DD6 - 248 - 26
51GLUGLULEULEU5EE6 - 248 - 26
61GLUGLULEULEU5FF6 - 248 - 26
71GLUGLULEULEU5GG6 - 248 - 26
81GLUGLULEULEU5HH6 - 248 - 26
12CYSCYSPHEPHE4AA34 - 4536 - 47
22CYSCYSPHEPHE4BB34 - 4536 - 47
32CYSCYSPHEPHE4CC34 - 4536 - 47
42CYSCYSPHEPHE4DD34 - 4536 - 47
52CYSCYSPHEPHE4EE34 - 4536 - 47
62CYSCYSPHEPHE4FF34 - 4536 - 47
72CYSCYSPHEPHE4GG34 - 4536 - 47
82CYSCYSPHEPHE4HH34 - 4536 - 47
13SERSERSERSER4AA57 - 6459 - 66
23SERSERSERSER4BB57 - 6459 - 66
33SERSERSERSER4CC57 - 6459 - 66
43SERSERSERSER4DD57 - 6459 - 66
53SERSERSERSER4EE57 - 6459 - 66
63SERSERSERSER4FF57 - 6459 - 66
73SERSERSERSER4GG57 - 6459 - 66
83SERSERSERSER4HH57 - 6459 - 66
14GLNGLNSERSER4AA67 - 7869 - 80
24GLNGLNSERSER4BB67 - 7869 - 80
34GLNGLNSERSER4CC67 - 7869 - 80
44GLNGLNSERSER4DD67 - 7869 - 80
54GLNGLNSERSER4EE67 - 7869 - 80
64GLNGLNSERSER4FF67 - 7869 - 80
74GLNGLNSERSER4GG67 - 7869 - 80
84GLNGLNSERSER4HH67 - 7869 - 80
15TYRTYRTHRTHR4AA81 - 9083 - 92
25TYRTYRTHRTHR4BB81 - 9083 - 92
35TYRTYRTHRTHR4CC81 - 9083 - 92
45TYRTYRTHRTHR4DD81 - 9083 - 92
55TYRTYRTHRTHR4EE81 - 9083 - 92
65TYRTYRTHRTHR4FF81 - 9083 - 92
75TYRTYRTHRTHR4GG81 - 9083 - 92
85TYRTYRTHRTHR4HH81 - 9083 - 92
16LYSLYSLEULEU4AA93 - 9795 - 99
26LYSLYSLEULEU4BB93 - 9795 - 99
36LYSLYSLEULEU4CC93 - 9795 - 99
46LYSLYSLEULEU4DD93 - 9795 - 99
56LYSLYSLEULEU4EE93 - 9795 - 99
66LYSLYSLEULEU4FF93 - 9795 - 99
76LYSLYSLEULEU4GG93 - 9795 - 99
86LYSLYSLEULEU4HH93 - 9795 - 99
17LEULEUGLYGLY4AA101 - 113103 - 115
27LEULEUGLYGLY4BB101 - 113103 - 115
37LEULEUGLYGLY4CC101 - 113103 - 115
47LEULEUGLYGLY4DD101 - 113103 - 115
57LEULEUGLYGLY4EE101 - 113103 - 115
67LEULEUGLYGLY4FF101 - 113103 - 115
77LEULEUGLYGLY4GG101 - 113103 - 115
87LEULEUGLYGLY4HH101 - 113103 - 115
18PHEPHEASPASP4AA139 - 160141 - 162
28PHEPHEASPASP4BB139 - 160141 - 162
38PHEPHEASPASP4CC139 - 160141 - 162
48PHEPHEASPASP4DD139 - 160141 - 162
58PHEPHEASPASP4EE139 - 160141 - 162
68PHEPHEASPASP4FF139 - 160141 - 162
78PHEPHEASPASP4GG139 - 160141 - 162
88PHEPHEASPASP4HH139 - 160141 - 162
19ARGARGLEULEU4AA189 - 195191 - 197
29ARGARGLEULEU4BB189 - 195191 - 197
39ARGARGLEULEU4CC189 - 195191 - 197
49ARGARGLEULEU4DD189 - 195191 - 197
59ARGARGLEULEU4EE189 - 195191 - 197
69ARGARGLEULEU4FF189 - 195191 - 197
79ARGARGLEULEU4GG189 - 195191 - 197
89ARGARGLEULEU4HH189 - 195191 - 197
110GLYGLYALAALA4AA209 - 220211 - 222
210GLYGLYALAALA4BB209 - 220211 - 222
310GLYGLYALAALA4CC209 - 220211 - 222
410GLYGLYALAALA4DD209 - 220211 - 222
510GLYGLYALAALA4EE209 - 220211 - 222
610GLYGLYALAALA4FF209 - 220211 - 222
710GLYGLYALAALA4GG209 - 220211 - 222
810GLYGLYALAALA4HH209 - 220211 - 222
111PHEPHEASPASP4AA223 - 241225 - 243
211PHEPHEASPASP4BB223 - 241225 - 243
311PHEPHEASPASP4CC223 - 241225 - 243
411PHEPHEASPASP4DD223 - 241225 - 243
511PHEPHEASPASP4EE223 - 241225 - 243
611PHEPHEASPASP4FF223 - 241225 - 243
711PHEPHEASPASP4GG223 - 241225 - 243
811PHEPHEASPASP4HH223 - 241225 - 243

NCS oper:
IDCodeMatrixVector
1given(0.591, -0.2919, -0.752), (-0.3082, -0.9432, 0.124), (-0.7455, 0.1585, -0.6474)0.3241, 2.7791, -0.4161
2given(0.9998, 0.0061, -0.0165), (0.0066, -0.9996, 0.0272), (-0.0163, -0.0273, -0.9995)-32.5448, 38.3717, -10.8344
3given(0.6062, 0.3174, 0.7292), (-0.2935, 0.9415, -0.1658), (-0.7392, -0.1135, 0.6639)-22.1826, -25.8703, 35.9779
4given(0.5355, -0.7834, -0.3154), (-0.8405, -0.4581, -0.2892), (0.0821, 0.42, -0.9038)-22.84, 41.8438, -81.9184
5given(0.5186, -0.635, 0.5726), (0.638, 0.7332, 0.2353), (-0.5692, 0.2433, 0.7854)34.7416, -41.5583, 76.0972
6given(0.5317, 0.7778, 0.3351), (-0.8424, 0.4449, 0.304), (0.0874, -0.4439, 0.8918)-72.5493, 64.9614, 100.1988
7given(0.5169, 0.6489, -0.5584), (0.6392, -0.7264, -0.2525), (-0.5695, -0.2264, -0.7902)-137.2589, -20.1594, -2.942

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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.: 8
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-AVU / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / arabinosyl-2-fluoro-deoxy-adenosine diphosphate ribose, ara-2'F-ADPR


Mass: 545.307 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H22FN5O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.47 % / 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: SSRF / Beamline: BL17U / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 100035 / % possible obs: 87.1 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.9 / % possible all: 70.1

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.454 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27689 4996 5 %RANDOM
Rwork0.21499 ---
obs0.21808 94519 87.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.304 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å2-0.13 Å20.29 Å2
2---1.21 Å21.98 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16113 0 280 294 16687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02216881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.98122916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93352002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96523.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.00715112
X-RAY DIFFRACTIONr_chiral_restr0.1230.22426
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112812
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_it0.8331.510049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.592216212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73536832
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4044.56704
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1047medium positional0.460.5
2B1047medium positional0.360.5
3C1047medium positional0.420.5
4D1047medium positional0.390.5
5E1047medium positional0.360.5
6F1047medium positional0.470.5
7G1047medium positional0.40.5
8H1047medium positional0.490.5
1A89loose positional0.275
2B89loose positional0.35
3C89loose positional0.355
4D89loose positional0.245
5E89loose positional0.275
6F89loose positional0.395
7G89loose positional0.335
8H89loose positional0.375
1A1047medium thermal1.272
2B1047medium thermal1.892
3C1047medium thermal1.362
4D1047medium thermal1.52
5E1047medium thermal1.272
6F1047medium thermal1.462
7G1047medium thermal1.152
8H1047medium thermal1.292
1A89loose thermal1.5910
2B89loose thermal1.9910
3C89loose thermal1.2210
4D89loose thermal1.6110
5E89loose thermal1.2610
6F89loose thermal1.5310
7G89loose thermal1.3310
8H89loose thermal1.3810
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 325 -
Rwork0.265 5606 -
obs--70.38 %
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)
12.04150.31930.00860.5409-0.1440.5971-0.01670.38180.0748-0.19530.11780.04550.0826-0.019-0.10110.1074-0.0463-0.00230.2205-0.00510.0829-8.3633-2.4089-12.5247
21.7342-0.17180.16240.5262-0.11741.4845-0.072-0.20540.0748-0.0042-0.0483-0.0095-0.0634-0.01530.12030.0118-0.00640.01590.1395-0.03770.12375.66215.500613.7763
31.3215-0.29920.25610.64240.04411.0206-0.1184-0.1466-0.14230.43880.18970.1192-0.0492-0.0615-0.07130.34010.08760.07490.14260.04790.086523.965140.98140.2999
41.4780.1756-0.04340.7855-0.07540.7166-0.06710.1048-0.07480.07380.04330.016-0.0048-0.04970.02380.03610.00520.00170.1643-0.00740.110337.668732.1239-26.04
50.7634-0.4204-0.05541.5698-1.13881.67530.0024-0.12150.0694-0.1470.1680.05450.1427-0.1494-0.17040.0227-0.0317-0.00940.13970.00420.111950.689337.979-54.3315
61.3152-0.42740.19681.5115-1.84922.5197-0.06360.21860.1151-0.75160.27480.15061.1862-0.3195-0.21110.6793-0.133-0.08040.18750.04330.060253.107834.4242-85.1812
70.84750.21250.51241.1519-0.99212.4174-0.11610.1471-0.09670.16410.0812-0.0601-0.2232-0.01710.03480.061-0.034-0.01550.1093-0.00830.117681.012270.0512-99.6204
81.0950.78480.32851.3888-0.8261.9826-0.1707-0.2159-0.06010.29530.08410.0066-0.8416-0.22290.08660.37870.0686-0.04880.17770.04980.109483.499573.0116-68.7751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 253
2X-RAY DIFFRACTION2B1 - 252
3X-RAY DIFFRACTION3C1 - 252
4X-RAY DIFFRACTION4D-1 - 250
5X-RAY DIFFRACTION5E1 - 252
6X-RAY DIFFRACTION6F1 - 252
7X-RAY DIFFRACTION7G1 - 252
8X-RAY DIFFRACTION8H1 - 252

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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