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

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Basic information

Entry
Database: PDB / ID: 3zww
TitleCrystal structure of ADP-ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.3 angstrom
ComponentsADP-RIBOSYL CYCLASECyclic ADP-ribose
KeywordsHYDROLASE / SUBSTRATE SPECIFICITY
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 1.3Feb 8, 2012Group: Other
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
Water6,720373
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)60.962, 77.522, 140.503
Angle α, β, γ (deg.)88.00, 89.16, 88.29
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 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA6 - 248 - 26
21GLUGLULEULEUBB6 - 248 - 26
31GLUGLULEULEUCC6 - 248 - 26
41GLUGLULEULEUDD6 - 248 - 26
51GLUGLULEULEUEE6 - 248 - 26
61GLUGLULEULEUFF6 - 248 - 26
71GLUGLULEULEUGG6 - 248 - 26
81GLUGLULEULEUHH6 - 248 - 26
12CYSCYSPHEPHEAA34 - 4536 - 47
22CYSCYSPHEPHEBB34 - 4536 - 47
32CYSCYSPHEPHECC34 - 4536 - 47
42CYSCYSPHEPHEDD34 - 4536 - 47
52CYSCYSPHEPHEEE34 - 4536 - 47
62CYSCYSPHEPHEFF34 - 4536 - 47
72CYSCYSPHEPHEGG34 - 4536 - 47
82CYSCYSPHEPHEHH34 - 4536 - 47
13SERSERSERSERAA57 - 6459 - 66
23SERSERSERSERBB57 - 6459 - 66
33SERSERSERSERCC57 - 6459 - 66
43SERSERSERSERDD57 - 6459 - 66
53SERSERSERSEREE57 - 6459 - 66
63SERSERSERSERFF57 - 6459 - 66
73SERSERSERSERGG57 - 6459 - 66
83SERSERSERSERHH57 - 6459 - 66
14GLNGLNSERSERAA67 - 7869 - 80
24GLNGLNSERSERBB67 - 7869 - 80
34GLNGLNSERSERCC67 - 7869 - 80
44GLNGLNSERSERDD67 - 7869 - 80
54GLNGLNSERSEREE67 - 7869 - 80
64GLNGLNSERSERFF67 - 7869 - 80
74GLNGLNSERSERGG67 - 7869 - 80
84GLNGLNSERSERHH67 - 7869 - 80
15TYRTYRTHRTHRAA81 - 9083 - 92
25TYRTYRTHRTHRBB81 - 9083 - 92
35TYRTYRTHRTHRCC81 - 9083 - 92
45TYRTYRTHRTHRDD81 - 9083 - 92
55TYRTYRTHRTHREE81 - 9083 - 92
65TYRTYRTHRTHRFF81 - 9083 - 92
75TYRTYRTHRTHRGG81 - 9083 - 92
85TYRTYRTHRTHRHH81 - 9083 - 92
16LYSLYSLEULEUAA93 - 9795 - 99
26LYSLYSLEULEUBB93 - 9795 - 99
36LYSLYSLEULEUCC93 - 9795 - 99
46LYSLYSLEULEUDD93 - 9795 - 99
56LYSLYSLEULEUEE93 - 9795 - 99
66LYSLYSLEULEUFF93 - 9795 - 99
76LYSLYSLEULEUGG93 - 9795 - 99
86LYSLYSLEULEUHH93 - 9795 - 99
17LEULEUGLYGLYAA101 - 113103 - 115
27LEULEUGLYGLYBB101 - 113103 - 115
37LEULEUGLYGLYCC101 - 113103 - 115
47LEULEUGLYGLYDD101 - 113103 - 115
57LEULEUGLYGLYEE101 - 113103 - 115
67LEULEUGLYGLYFF101 - 113103 - 115
77LEULEUGLYGLYGG101 - 113103 - 115
87LEULEUGLYGLYHH101 - 113103 - 115
18PHEPHEASPASPAA139 - 160141 - 162
28PHEPHEASPASPBB139 - 160141 - 162
38PHEPHEASPASPCC139 - 160141 - 162
48PHEPHEASPASPDD139 - 160141 - 162
58PHEPHEASPASPEE139 - 160141 - 162
68PHEPHEASPASPFF139 - 160141 - 162
78PHEPHEASPASPGG139 - 160141 - 162
88PHEPHEASPASPHH139 - 160141 - 162
19ARGARGLEULEUAA189 - 195191 - 197
29ARGARGLEULEUBB189 - 195191 - 197
39ARGARGLEULEUCC189 - 195191 - 197
49ARGARGLEULEUDD189 - 195191 - 197
59ARGARGLEULEUEE189 - 195191 - 197
69ARGARGLEULEUFF189 - 195191 - 197
79ARGARGLEULEUGG189 - 195191 - 197
89ARGARGLEULEUHH189 - 195191 - 197
110GLYGLYALAALAAA209 - 220211 - 222
210GLYGLYALAALABB209 - 220211 - 222
310GLYGLYALAALACC209 - 220211 - 222
410GLYGLYALAALADD209 - 220211 - 222
510GLYGLYALAALAEE209 - 220211 - 222
610GLYGLYALAALAFF209 - 220211 - 222
710GLYGLYALAALAGG209 - 220211 - 222
810GLYGLYALAALAHH209 - 220211 - 222
111PHEPHEASPASPAA223 - 241225 - 243
211PHEPHEASPASPBB223 - 241225 - 243
311PHEPHEASPASPCC223 - 241225 - 243
411PHEPHEASPASPDD223 - 241225 - 243
511PHEPHEASPASPEE223 - 241225 - 243
611PHEPHEASPASPFF223 - 241225 - 243
711PHEPHEASPASPGG223 - 241225 - 243
811PHEPHEASPASPHH223 - 241225 - 243

NCS oper:
IDCodeMatrixVector
1given(0.607, -0.3369, -0.7197), (-0.3357, -0.9296, 0.152), (-0.7203, 0.1494, -0.6774)0.0622, -0.3706, -0.0442
2given(0.5936, 0.303, 0.7455), (-0.3462, 0.9325, -0.1033), (-0.7265, -0.1967, 0.6584)-18.4903, -24.1579, 36.8909
3given(0.9998, -0.0087, 0.0186), (-0.008, -0.9991, -0.0407), (0.0189, 0.0406, -0.999)-29.079, 34.679, -15.0017
4given(0.5292, 0.7925, 0.3033), (-0.8401, 0.439, 0.3188), (0.1195, -0.4235, 0.898)-28.7805, -0.5981, -53.3254
5given(0.531, 0.6278, -0.5691), (0.6096, -0.7496, -0.258), (-0.5886, -0.2099, -0.7807)20.8768, 1.9882, 56.8459
6given(0.5174, -0.7871, -0.3358), (-0.8455, -0.4099, -0.3421), (0.1316, 0.4609, -0.8776)-20.2757, 35.0492, -85.0458
7given(0.5213, -0.6558, 0.546), (0.6172, 0.7316, 0.2895), (-0.5893, 0.1861, 0.7862)35.8454, -39.2081, 77.8034

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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.: 373 / 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: 2.9 Å3/Da / Density % sol: 57.62 % / 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: 106984 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.2 / % possible all: 83.6

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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→29.86 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.194 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25736 5356 5 %RANDOM
Rwork0.19977 ---
obs0.20269 101533 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.12 Å2
2--0.05 Å20.19 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16116 0 280 373 16769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02216884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9822916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6352004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14723.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.811152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.05815112
X-RAY DIFFRACTIONr_chiral_restr0.1270.22428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112792
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_it0.8731.510052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.736216212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.05236832
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8844.56704
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
1A556medium positional0.160.5
2B556medium positional0.160.5
3C556medium positional0.150.5
4D556medium positional0.180.5
5E556medium positional0.170.5
6F556medium positional0.20.5
7G556medium positional0.190.5
8H556medium positional0.270.5
1A580loose positional0.525
2B580loose positional0.455
3C580loose positional0.375
4D580loose positional0.445
5E580loose positional0.375
6F580loose positional0.415
7G580loose positional0.455
8H580loose positional0.485
1A556medium thermal0.992
2B556medium thermal1.642
3C556medium thermal1.192
4D556medium thermal1.172
5E556medium thermal0.922
6F556medium thermal0.942
7G556medium thermal0.962
8H556medium thermal1.032
1A580loose thermal1.1810
2B580loose thermal1.710
3C580loose thermal1.4210
4D580loose thermal1.4110
5E580loose thermal1.3710
6F580loose thermal1.1310
7G580loose thermal1.2410
8H580loose thermal1.2410
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 243 -
Rwork0.278 5156 -
obs--64.07 %
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)
12.13480.2532-0.28560.6958-0.18621.1244-0.16820.38660.1204-0.39510.25040.08030.0595-0.1499-0.08220.2643-0.1435-0.04330.1390.0390.1115-6.7325-4.8683-13.1253
21.848-0.20060.21190.9816-0.0091.0592-0.0631-0.15250.0662-0.05210.06750.0465-0.02-0.0958-0.00440.0106-0.007-0.00920.04240.00840.11667.11334.415613.0889
31.82920.3699-0.41360.6925-0.21721.6835-0.08320.2285-0.0666-0.01190.00810.00350.125-0.0730.07510.0147-0.0182-0.00680.1085-0.04070.104736.783131.5079-26.0733
42.0543-0.2176-0.44660.9413-0.11050.8759-0.0071-0.2377-0.02620.27750.11030.0445-0.06280.0891-0.10320.11360.02230.00080.0858-0.02360.096422.690239.45820.233
50.91540.34820.12841.5852-0.88991.6521-0.0044-0.0492-0.07050.15620.18450.0202-0.086-0.1578-0.18010.02240.0345-0.00940.09570.01630.094120.072-1.37141.271
60.82810.2732-0.16411.413-1.75432.3363-0.0173-0.33890.00970.68570.20650.1182-0.9608-0.2379-0.18910.54580.15540.03950.316-0.00750.125422.48952.586772.1902
71.0068-0.2733-0.5961.0304-0.67662.4896-0.0999-0.03850.0741-0.12310.0129-0.07980.1527-0.03480.0870.03880.01670.00070.0934-0.01210.090950.282138.7695-53.9071
81.0251-0.68010.04861.4645-1.05862.1945-0.07180.36060.0012-0.2599-0.0110.0350.6547-0.1580.08280.2951-0.01080.04980.23080.01870.148252.746136.0256-84.8827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 252
2X-RAY DIFFRACTION2B1 - 251
3X-RAY DIFFRACTION3C1 - 251
4X-RAY DIFFRACTION4D1 - 251
5X-RAY DIFFRACTION5E1 - 251
6X-RAY DIFFRACTION6F0 - 251
7X-RAY DIFFRACTION7G1 - 251
8X-RAY DIFFRACTION8H0 - 251

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