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- PDB-3rom: Crystal structure of human CD38 in complex with compound CZ-48 -

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Basic information

Entry
Database: PDB / ID: 3rom
TitleCrystal structure of human CD38 in complex with compound CZ-48
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / inhibitory compound / covalent intermediate / CZ-48 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to hydroperoxide / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / apoptotic signaling pathway / response to progesterone / female pregnancy / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear 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-48Z / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: Biochemistry / Year: 2012
Title: Catalysis-based inhibitors of the calcium signaling function of CD38.
Authors: Kwong, A.K. / Chen, Z. / Zhang, H. / Leung, F.P. / Lam, C.M. / Ting, K.Y. / Zhang, L. / Hao, Q. / Zhang, L.H. / Lee, H.C.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references / Non-polymer description
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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _chem_comp.type ..._chem_comp.pdbx_synonyms / _chem_comp.type / _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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5754
Polymers59,0792
Non-polymers4962
Water4,270237
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7882
Polymers29,5391
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7882
Polymers29,5391
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.914, 50.847, 68.617
Angle α, β, γ (deg.)65.210, 83.600, 82.520
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 29539.479 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 45-296) / Mutation: N100D, N164D, N219D, N209D
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: Sugar ChemComp-48Z / 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose


Type: D-saccharide, alpha linking / Mass: 248.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10FO6PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE REAL LEAVING GROUP NICOTINAMIDE OF LIGAND 48Z CAN NOT BE SEEN IN THE STRUCTURE
Sequence detailsQ -> T AT THIS POSITION IN GENBANK AAA68482

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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: 1.101 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 31537 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.399 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.123.40.38431080.982196.8
2.12-2.213.50.28231550.925297
2.21-2.313.50.23231331.008397.9
2.31-2.433.50.17731560.897497.9
2.43-2.583.50.14131521.02597.9
2.58-2.783.50.10831621.104698.1
2.78-3.063.50.08431691.338798.6
3.06-3.513.50.06431971.865898.6
3.51-4.423.40.04831892.425999.2
4.42-503.30.03931162.5041096.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1yh3


Resolution: 2.04→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2306 / WRfactor Rwork: 0.1854 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8529 / SU B: 10.363 / SU ML: 0.129 / SU R Cruickshank DPI: 0.2258 / SU Rfree: 0.1816 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1583 5 %RANDOM
Rwork0.1829 ---
obs0.1851 31515 97.18 %-
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: 52.69 Å2 / Biso mean: 38.506 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.28 Å2-0.67 Å2
2---0.52 Å20.75 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 26 237 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224232
X-RAY DIFFRACTIONr_bond_other_d0.0010.022910
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9415742
X-RAY DIFFRACTIONr_angle_other_deg0.7993.0017053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3055503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14524.146205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8921528
X-RAY DIFFRACTIONr_chiral_restr0.0670.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
X-RAY DIFFRACTIONr_mcbond_it0.4011.52527
X-RAY DIFFRACTIONr_mcbond_other0.0961.51004
X-RAY DIFFRACTIONr_mcangle_it0.79724118
X-RAY DIFFRACTIONr_scbond_it1.42931705
X-RAY DIFFRACTIONr_scangle_it2.2554.51624
LS refinement shellResolution: 2.039→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 88 -
Rwork0.228 2016 -
all-2104 -
obs--87.96 %
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)
17.63092.0667-0.83224.3988-1.15742.97550.26280.280.8463-0.00380.13590.8578-0.2194-0.1762-0.39860.19060.02870.01620.04030.05360.45564.38216.0252.001
24.18575.14010.08026.42690.30060.45120.551-0.35250.51310.6346-0.40.5363-0.08670.0171-0.15110.16390.00690.03840.1417-0.06080.2521-0.6233.0919.429
35.61790.54413.06435.60663.68223.74610.15190.43080.3484-0.3113-0.380.1584-0.0993-0.06640.22810.2041-0.0024-0.03650.25010.15490.2567-7.0061.358-2.424
44.4462.551-1.77556.6806-1.92383.4703-0.00020.22010.0577-0.3686-0.0155-0.34540.08420.30340.01580.10630.02870.0050.1163-0.00370.165212.94110.1010.891
55.14090.3207-0.5173.27870.72365.9042-0.00430.42230.0231-0.24440.0152-0.2109-0.03680.2889-0.01090.07460.02550.00920.0648-0.00260.08640.107-11.1540.053
63.3549-0.34440.7073.0617-0.15042.7520.13170.4056-0.3826-0.34480.08780.36570.1523-0.2688-0.21960.1509-0.02070.01410.219-0.05680.1453-6.686-15.173-5.134
74.4295-0.29530.7754.2764-3.77658.30210.056-0.5022-0.57290.1638-0.1234-0.29870.43120.32490.06740.08240.0175-0.02130.1070.01950.230427.072-19.81519.647
81.99510.8270.83531.30591.03464.28640.2042-0.5588-0.47160.3474-0.1056-0.13890.5232-0.3107-0.09860.1829-0.0385-0.01930.23220.09460.187416.173-20.74925.558
95.26113.42953.32439.6445.48826.40060.0646-0.51020.01540.64950.3568-0.47190.01040.1687-0.42140.21380.0122-0.01640.42960.05660.229126.298-10.58736.783
105.45910.20260.38672.3451-0.38084.04490.0348-0.1288-0.0005-0.0439-0.0506-0.0207-0.2092-0.15810.01580.02610.0034-0.00820.0483-0.00930.073919.127-13.63816.116
115.54572.63961.80916.07541.47933.3163-0.05250.18370.2369-0.3398-0.19090.2287-0.0307-0.39010.24340.24770.01590.03480.4146-0.04710.111914.07-3.59936.106
124.98150.7322-0.17824.8605-0.45172.64050.0421-0.11050.45690.2504-0.2499-0.3274-0.15090.20140.20780.3709-0.04570.00310.4379-0.05330.155122.114.76242.255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 100
2X-RAY DIFFRACTION2A101 - 126
3X-RAY DIFFRACTION3A127 - 154
4X-RAY DIFFRACTION4A155 - 193
5X-RAY DIFFRACTION5A194 - 254
6X-RAY DIFFRACTION6A255 - 296
7X-RAY DIFFRACTION7B44 - 79
8X-RAY DIFFRACTION8B80 - 126
9X-RAY DIFFRACTION9B127 - 150
10X-RAY DIFFRACTION10B151 - 193
11X-RAY DIFFRACTION11B194 - 244
12X-RAY DIFFRACTION12B245 - 296

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