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- PDB-3zwx: Crystal structure of ADP-ribosyl cyclase complexed with 8-bromo-A... -

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Basic information

Entry
Database: PDB / ID: 3zwx
TitleCrystal structure of ADP-ribosyl cyclase complexed with 8-bromo-ADP- ribose
ComponentsADP-RIBOSYL CYCLASECyclic ADP-ribose
KeywordsHYDROLASE / CD38 / 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 / cytoplasmic vesicle / transferase activity / 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-AV1 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKotaka, M. / Graeff, R. / Zhang, L.H. / Lee, H.C. / Hao, Q.
CitationJournal: To be Published
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 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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_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_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)242,89620
Polymers237,7778
Non-polymers5,12012
Water5,639313
1
A: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7245
Polymers59,4442
Non-polymers1,2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-20.9 kcal/mol
Surface area23460 Å2
MethodPISA
2
C: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7245
Polymers59,4442
Non-polymers1,2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-18.3 kcal/mol
Surface area23820 Å2
MethodPISA
3
E: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7245
Polymers59,4442
Non-polymers1,2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-22 kcal/mol
Surface area23790 Å2
MethodPISA
4
G: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7245
Polymers59,4442
Non-polymers1,2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21.5 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.682, 76.818, 140.333
Angle α, β, γ (deg.)87.85, 89.25, 89.12
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
11LEULEUARGARGAA7 - 229 - 24
21LEULEUARGARGBB7 - 229 - 24
31LEULEUARGARGCC7 - 229 - 24
41LEULEUARGARGDD7 - 229 - 24
51LEULEUARGARGEE7 - 229 - 24
61LEULEUARGARGFF7 - 229 - 24
71LEULEUARGARGGG7 - 229 - 24
81LEULEUARGARGHH7 - 229 - 24
12CYSCYSSERSERAA34 - 4636 - 48
22CYSCYSSERSERBB34 - 4636 - 48
32CYSCYSSERSERCC34 - 4636 - 48
42CYSCYSSERSERDD34 - 4636 - 48
52CYSCYSSERSEREE34 - 4636 - 48
62CYSCYSSERSERFF34 - 4636 - 48
72CYSCYSSERSERGG34 - 4636 - 48
82CYSCYSSERSERHH34 - 4636 - 48
13TYRTYRGLNGLNAA58 - 6660 - 68
23TYRTYRGLNGLNBB58 - 6660 - 68
33TYRTYRGLNGLNCC58 - 6660 - 68
43TYRTYRGLNGLNDD58 - 6660 - 68
53TYRTYRGLNGLNEE58 - 6660 - 68
63TYRTYRGLNGLNFF58 - 6660 - 68
73TYRTYRGLNGLNGG58 - 6660 - 68
83TYRTYRGLNGLNHH58 - 6660 - 68
14ASNASNGLYGLYAA72 - 11374 - 115
24ASNASNGLYGLYBB72 - 11374 - 115
34ASNASNGLYGLYCC72 - 11374 - 115
44ASNASNGLYGLYDD72 - 11374 - 115
54ASNASNGLYGLYEE72 - 11374 - 115
64ASNASNGLYGLYFF72 - 11374 - 115
74ASNASNGLYGLYGG72 - 11374 - 115
84ASNASNGLYGLYHH72 - 11374 - 115
15TRPTRPGLYGLYAA140 - 161142 - 163
25TRPTRPGLYGLYBB140 - 161142 - 163
35TRPTRPGLYGLYCC140 - 161142 - 163
45TRPTRPGLYGLYDD140 - 161142 - 163
55TRPTRPGLYGLYEE140 - 161142 - 163
65TRPTRPGLYGLYFF140 - 161142 - 163
75TRPTRPGLYGLYGG140 - 161142 - 163
85TRPTRPGLYGLYHH140 - 161142 - 163
16ARGARGALAALAAA189 - 245191 - 247
26ARGARGALAALABB189 - 245191 - 247
36ARGARGALAALACC189 - 245191 - 247
46ARGARGALAALADD189 - 245191 - 247
56ARGARGALAALAEE189 - 245191 - 247
66ARGARGALAALAFF189 - 245191 - 247
76ARGARGALAALAGG189 - 245191 - 247
86ARGARGALAALAHH189 - 245191 - 247

NCS oper:
IDCodeMatrixVector
1given(0.5945, 0.3077, 0.7429), (0.282, -0.945, 0.1657), (0.7531, 0.111, -0.6485)0.0789, -0.5575, 0.0831
2given(0.602, -0.3247, -0.7295), (0.2929, 0.9397, -0.1765), (0.7428, -0.1074, 0.6608)15.4531, 43.6245, 8.9304
3given(0.9998, 0.0185, 0.0105), (0.0181, -0.9992, 0.0368), (0.0112, -0.0366, -0.9993)29.2998, -35.4979, 12.2426
4given(0.5078, 0.6419, -0.5746), (-0.657, 0.72, 0.2237), (0.5573, 0.2639, 0.7873)66.3031, 4.1577, -41.4091
5given(0.5382, 0.7814, 0.3159), (0.8406, -0.4705, -0.2683), (-0.061, 0.41, -0.9101)9.4405, 8.7421, 77.4058
6given(0.499, -0.6643, 0.5565), (-0.6635, -0.7059, -0.2478), (0.5574, -0.2456, -0.7931)21.4585, 1.1892, -56.3363
7given(0.5293, -0.7788, -0.3365), (0.8459, 0.4537, 0.2804), (-0.0657, -0.4331, 0.8989)-29.1899, -3.219, 52.7284

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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) / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-AV1 / [(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / 8-BROMOADENOSINE-5'-O-DIPHOSPHORIBOSE


Mass: 622.212 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H22BrN5O13P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.86 Å3/Da / Density % sol: 56.97 % / 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 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 75158 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1

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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
Resolution: 2.6→29.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 28.955 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 1.055 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27148 3763 5 %RANDOM
Rwork0.20289 ---
obs0.20635 71392 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.472 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.06 Å2-0.06 Å2
2--0.11 Å20.23 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16124 0 292 313 16729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.98322940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60952004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85223.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.929152808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.28615112
X-RAY DIFFRACTIONr_chiral_restr0.1170.22444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112800
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_it0.6041.510052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.229216214
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11136840
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5544.56726
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
1A636medium positional0.180.5
2B636medium positional0.220.5
3C636medium positional0.190.5
4D636medium positional0.190.5
5E636medium positional0.20.5
6F636medium positional0.230.5
7G636medium positional0.230.5
8H636medium positional0.260.5
1A633loose positional0.45
2B633loose positional0.485
3C633loose positional0.455
4D633loose positional0.485
5E633loose positional0.455
6F633loose positional0.55
7G633loose positional0.515
8H633loose positional0.645
1A636medium thermal0.682
2B636medium thermal0.642
3C636medium thermal0.552
4D636medium thermal0.822
5E636medium thermal0.742
6F636medium thermal0.662
7G636medium thermal0.622
8H636medium thermal0.622
1A633loose thermal0.9810
2B633loose thermal0.9510
3C633loose thermal0.8710
4D633loose thermal1.0310
5E633loose thermal0.9310
6F633loose thermal0.8810
7G633loose thermal0.8710
8H633loose thermal0.8510
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 236 -
Rwork0.295 4766 -
obs--87.39 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.49960.4585-0.45160.5216-0.04551.4628-0.09510.24070.1381-0.04210.05470.08040.0505-0.07820.04040.01170.0024-0.0090.1123-0.01910.14087.1278-4.1386-13.1645
21.7665-0.20090.19580.3828-0.20120.5970.0019-0.2195-0.20410.13840.08660.0379-0.0002-0.035-0.08850.12920.00620.01520.1337-0.04160.134-6.86974.025413.3404
31.950.0808-0.35210.6429-0.02360.602-0.060.13490.2186-0.27610.09540.1118-0.0906-0.09-0.03540.2714-0.0474-0.07140.0813-0.00460.1703-35.5464-39.73730.089
41.2785-0.3770.38150.7295-0.07141.0093-0.0807-0.2335-0.1255-0.00870.03560.08930.0098-0.160.04520.0204-0.02180.01780.15-0.02180.1454-21.8634-30.933726.3435
50.49740.42520.29821.8052-0.90271.60160.0264-0.0299-0.0240.19980.11480.1068-0.1572-0.206-0.14120.02880.00370.00650.1469-0.00940.1405-8.782-36.515954.3617
61.09040.14680.04230.8519-0.9311.58-0.1294-0.2288-0.15690.43930.2125-0.038-0.6781-0.2569-0.0830.44670.11180.02860.2633-0.01420.155-6.7083-33.011585.144
70.405-0.4637-0.34421.4528-0.70431.9138-0.0340.0536-0.0173-0.11960.01590.04090.1884-0.12660.01820.0389-0.01170.02260.1352-0.03080.14420.38412.7486-40.8867
80.9891-0.8696-0.1061.3098-0.74811.4491-0.07340.17260.1615-0.23060.0019-0.13120.5437-0.16650.07150.3541-0.05480.03410.25240.00310.161422.819-0.0697-71.7554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B0 - 251
3X-RAY DIFFRACTION3C1 - 252
4X-RAY DIFFRACTION4D-1 - 250
5X-RAY DIFFRACTION5E1 - 251
6X-RAY DIFFRACTION6F1 - 252
7X-RAY DIFFRACTION7G-1 - 251
8X-RAY DIFFRACTION8H0 - 251

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