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- PDB-3ofs: Dynamic conformations of the CD38-mediated NAD cyclization captur... -

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Basic information

Entry
Database: PDB / ID: 3ofs
TitleDynamic conformations of the CD38-mediated NAD cyclization captured using multi-copy crystallography
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / CD38 / cyclization / hydrolysis / cADPR / ADPR / ara-2'F-NAD / ara-2'F-ADPR
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / positive regulation of vasoconstriction / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / response to interleukin-1 / response to progesterone / B cell receptor signaling pathway / apoptotic signaling pathway / female pregnancy / positive regulation of insulin secretion / response to estradiol / negative regulation of neuron projection development / transferase activity / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / nuclear membrane / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / 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-AVU / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Dynamic Conformations of the CD38-Mediated NAD Cyclization Captured in a Single Crystal
Authors: Zhang, H. / Graeff, R. / Chen, Z. / Zhang, L.R. / Zhang, L.H. / Lee, H.C. / Hao, Q.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
C: ADP-ribosyl cyclase 1
D: ADP-ribosyl cyclase 1
E: ADP-ribosyl cyclase 1
F: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,80012
Polymers178,5286
Non-polymers3,2726
Water7,062392
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3002
Polymers29,7551
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.655, 146.662, 191.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ADP-ribosyl cyclase 1 / CD38 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 29754.703 Da / Num. of mol.: 6 / Fragment: extracellular domain, residues 46-300 / Mutation: Q49T, N100D, E146A, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P28907, 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.: 6 / Source method: obtained synthetically / Formula: C15H22FN5O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.22 Å3/Da / Density % sol: 44.68 % / Mosaicity: 0.516 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH 4.0, 15% PEG 4000, 0.2M ammonium acetate, 3% isopropanol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97623 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 79445 / % possible obs: 97.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.095 / Χ2: 1.247 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.284.60.35472080.92789.9
2.28-2.375.10.31576130.97395
2.37-2.485.70.29977491.00496.7
2.48-2.616.40.24779431.0798.6
2.61-2.777.10.21480171.199.3
2.77-2.997.70.17780571.07699.5
2.99-3.2980.12980471.08899.7
3.29-3.768.40.181641.38699.7
3.76-4.748.70.0881951.71499.6
4.74-1008.40.0684521.58298.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3

1yh3


Resolution: 2.2→48.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.2077 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8284 / SU B: 14.383 / SU ML: 0.17 / SU R Cruickshank DPI: 0.3024 / SU Rfree: 0.2246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 3969 5 %RANDOM
Rwork0.2033 ---
obs0.2057 79380 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.13 Å2 / Biso mean: 47.9 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--1.99 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 210 392 11948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211898
X-RAY DIFFRACTIONr_bond_other_d0.0010.028047
X-RAY DIFFRACTIONr_angle_refined_deg1.171.95416190
X-RAY DIFFRACTIONr_angle_other_deg0.8223.00119431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50151396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47624.007554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.316152003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.111573
X-RAY DIFFRACTIONr_chiral_restr0.0680.21774
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022398
X-RAY DIFFRACTIONr_mcbond_it0.4451.57026
X-RAY DIFFRACTIONr_mcbond_other0.0951.52800
X-RAY DIFFRACTIONr_mcangle_it0.861211436
X-RAY DIFFRACTIONr_scbond_it1.48934872
X-RAY DIFFRACTIONr_scangle_it2.3464.54754
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 246 -
Rwork0.24 4700 -
all-4946 -
obs--82.99 %
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)
14.1006-0.0154-1.10572.73570.50255.7186-0.1521-0.2644-0.0530.068-0.05080.1387-0.5105-0.15580.2030.101-0.0376-0.04880.24270.01570.1738-38.6514.913-1.408
26.7477-5.8977-2.161911.81872.00966.2358-0.31470.0563-1.00340.6128-0.08571.06190.5519-0.80790.40030.2381-0.04720.05020.30680.02810.3303-30.82-3.48817.513
33.84570.93630.77832.4390.83247.7982-0.21860.2132-0.3484-0.0326-0.0288-0.3276-0.09870.57430.24750.0481-0.0799-0.00010.23980.03570.2129-30.5051.847-3.365
46.5454-1.86110.7198.1455-0.45554.3828-0.2795-0.0917-0.26530.15230.0071-0.5074-0.04310.46560.27250.1179-0.0185-0.00130.30120.10310.1991-17.437-1.63818.238
54.4481-0.97990.77872.9294-0.34666.9934-0.01910.25380.0649-0.2392-0.10940.3313-0.0361-1.00710.12860.17270.0482-0.00520.33230.00670.2597-10.19218.143.348
65.51984.68672.25067.2766-0.94877.4089-0.44930.14420.80420.01910.13481.0096-1.2724-0.75350.31450.4484-0.0121-0.09230.31510.05160.2911-1.79526.537-15.96
73.365-0.6067-0.93892.55021.12189.3361-0.0015-0.08550.3401-0.0579-0.0679-0.2124-0.6395-0.03780.06930.20440.0363-0.00830.10930.03960.1994-2.19421.2345.252
83.64021.6777-0.58288.7669-3.32826.5228-0.2365-0.09550.07080.0675-0.3721-0.6933-0.45390.90650.60850.2276-0.1648-0.08210.35520.12340.210711.45524.224-16.618
95.5780.0679-1.1044.10131.30994.7494-0.15610.1413-0.00280.0288-0.01680.043-0.4179-0.09270.17290.1748-0.0235-0.01290.0965-0.03690.2065-8.56422.961-46.745
108.0121.08362.02435.9984-0.4763.358-0.2468-0.53090.52530.3195-0.01670.6666-0.2348-0.84370.26350.157-0.0220.04180.2796-0.05010.2538-18.75713.114-30.447
114.2272-1.67610.24843.40930.17888.9657-0.14350.7471-0.5737-0.3527-0.13260.25080.1751-0.41760.27610.0838-0.06640.02480.204-0.13080.2692-10.73715.782-51.804
125.18431.0418-1.28833.6342-0.67262.9745-0.1564-0.052-0.3638-0.0406-0.0957-0.08660.3393-0.47110.25210.1783-0.10860.03650.1906-0.04640.2149-14.3710.108-29.302
134.11270.5008-2.19893.8674-1.81537.73160.29340.0910.267-0.2088-0.181-0.1289-0.5153-0.0604-0.11240.20910.0210.07990.01330.00790.2189.062-0.112-46.183
1411.87470.54370.39843.68852.05062.6662-0.17410.60590.7099-0.1170.1419-0.522-0.25830.78210.03230.3003-0.0150.04560.3870.16930.268819.512-9.8-62.944
152.88531.5989-1.71192.3742-0.419612.4418-0.0146-0.2848-0.20560.102-0.1875-0.28040.62720.45370.20220.16270.04850.06210.04630.05350.199611.352-7.345-41.29
166.6643-1.5772-1.67963.29560.48254.751-0.27370.0799-0.90070.3504-0.01710.24050.61570.02450.29090.33730.02120.09350.0670.03770.277514.399-22.658-63.747
176.32750.75570.73524.5859-1.13746.5853-0.35320.41140.1865-0.36360.25350.25720.6283-0.92150.09960.1426-0.16010.00760.2644-0.03440.1452-10.843-29.9383.017
187.01326.4909-1.600313.72261.82445.0155-0.22670.8281.0067-0.79960.27840.97140.2326-1.5072-0.05170.2814-0.2314-0.08610.62760.13810.2544-2.821-20.603-15.782
195.46071.1164-0.61564.4122-2.66712.2638-0.5307-0.03270.4001-0.06090.1978-0.33810.16570.0080.33290.0898-0.0386-0.02670.0727-0.05670.1716-3.06-26.8725.295
203.27931.1143-1.7116.4371.19896.161-0.20450.179-0.0725-0.09670.065-0.34090.6556-0.19760.13950.1934-0.1118-0.01910.2110.02770.124410.364-23.01-16.391
212.9360.00210.13767.68253.931810.4451-0.006-0.12760.30210.1834-0.48180.3316-1.0141-0.5930.48770.34530.0482-0.07970.0777-0.04010.2727-11.808-24.097-50.034
223.12470.93190.995512.63913.269510.3454-0.035-0.0328-0.03750.1347-0.2577-0.4537-0.67560.57230.29270.1668-0.0897-0.05150.06580.06310.185-1.693-29.099-50.422
231.61213.913-3.285610.2542-9.02958.16980.6017-0.14650.47772.13220.14260.9805-2.0842-0.4671-0.74430.99340.170.18320.5073-0.25890.2974-16.082-32.643-35.674
249.30561.41321.531913.5952.4416.76350.22130.4155-0.4093-0.1929-0.43350.26350.2991-0.25010.21220.2566-0.0056-0.04730.1407-0.06440.1686-10.12-34.839-60.724
251.69112.3496-4.30614.7837-6.429111.11180.0065-0.2083-0.3020.4233-0.7132-0.2724-0.11330.6950.70670.2461-0.12050.00460.2476-0.04090.2143-9.8-42.617-37.675
2610.75680.5606-0.30234.6756-1.63069.4731-0.0586-0.3021-0.58060.2333-0.20870.13820.0579-0.10680.26740.3231-0.1290.14690.1287-0.10780.1671-18.204-50.689-27.567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 114
2X-RAY DIFFRACTION2A115 - 145
3X-RAY DIFFRACTION3A146 - 194
4X-RAY DIFFRACTION4A195 - 281
5X-RAY DIFFRACTION5B46 - 114
6X-RAY DIFFRACTION6B115 - 144
7X-RAY DIFFRACTION7B145 - 194
8X-RAY DIFFRACTION8B195 - 281
9X-RAY DIFFRACTION9C46 - 115
10X-RAY DIFFRACTION10C116 - 147
11X-RAY DIFFRACTION11C148 - 192
12X-RAY DIFFRACTION12C193 - 281
13X-RAY DIFFRACTION13D46 - 116
14X-RAY DIFFRACTION14D117 - 147
15X-RAY DIFFRACTION15D148 - 192
16X-RAY DIFFRACTION16D193 - 280
17X-RAY DIFFRACTION17E46 - 114
18X-RAY DIFFRACTION18E115 - 144
19X-RAY DIFFRACTION19E145 - 192
20X-RAY DIFFRACTION20E193 - 281
21X-RAY DIFFRACTION21F46 - 81
22X-RAY DIFFRACTION22F82 - 114
23X-RAY DIFFRACTION23F115 - 159
24X-RAY DIFFRACTION24F160 - 179
25X-RAY DIFFRACTION25F180 - 235
26X-RAY DIFFRACTION26F236 - 280

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