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Basic information

Entry
Database: PDB / ID: 4tmf
TitleCrystal structure of human CD38 in complex with hydrolysed compound JMS713
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHydrolase/Hydrolase Inhibitor / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / inhibitory compound / JMS713 / 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-JS2 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsZhang, H. / Swarbrick, J. / Potter, B. / Hao, Q.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Cyclic adenosine 5'-diphosphate ribose analogs without a "southern" ribose inhibit ADP-ribosyl cyclase-hydrolase CD38.
Authors: Swarbrick, J.M. / Graeff, R. / Zhang, H. / Thomas, M.P. / Hao, Q. / Potter, B.V.
History
DepositionJun 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6564
Polymers59,6252
Non-polymers1,0312
Water1,44180
1
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3282
Polymers29,8131
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3282
Polymers29,8131
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.690, 54.128, 63.319
Angle α, β, γ (deg.)108.580, 90.980, 93.980
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 48 - 290 / Label seq-ID: 5 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer. And there are 2 biological units in the asymmetric unit (chain A and chain B).

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Components

#1: Protein ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose ...2'-phospho-ADP-ribosyl cyclase / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / 2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase 1 / ADPRC 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 29812.738 Da / Num. of mol.: 2 / Fragment: ecto domain / Mutation: N100D, N164A, 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, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
#2: Sugar ChemComp-JS2 / 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D- ribofuranose / 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D- ribose / 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-D-ribose / 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-ribose


Type: D-saccharide, alpha linking / Mass: 515.306 Da / Num. of mol.: 2 / Fragment: JMS713 / Source method: obtained synthetically / Formula: C14H23N5O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.26 Å3/Da / Density % sol: 45.67 % / Description: plate
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% PEG10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 31966 / % possible obs: 97.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Χ2: 0.994 / Net I/av σ(I): 24.624 / Net I/σ(I): 14.8 / Num. measured all: 126045
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.123.90.52831880.98997.3
2.12-2.2140.36232050.97997.3
2.21-2.3140.25232001.0397.6
2.31-2.4340.17832061.07697.7
2.43-2.5840.11831971.08197.9
2.58-2.7840.08132121.14398.3
2.78-3.0640.05632150.92498.5
3.06-3.513.90.0432440.93698.6
3.51-4.423.90.03331550.92596.7
4.42-503.90.03331440.85195.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3


Resolution: 2.05→47.12 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2451 / WRfactor Rwork: 0.2129 / FOM work R set: 0.8397 / SU B: 10.297 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2258 / SU Rfree: 0.1756 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1638 5.1 %RANDOM
Rwork0.198 30312 --
obs0.1996 31950 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 141.66 Å2 / Biso mean: 67.282 Å2 / Biso min: 33.18 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å2-2 Å2-0.3 Å2
2--2.67 Å21.53 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 2.05→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 66 80 4092
Biso mean--69.51 51.98 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024126
X-RAY DIFFRACTIONr_bond_other_d0.0050.023809
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9565609
X-RAY DIFFRACTIONr_angle_other_deg1.1273.018779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84224.388196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17115709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.581523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214550
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02953
X-RAY DIFFRACTIONr_mcbond_it1.522.7971940
X-RAY DIFFRACTIONr_mcbond_other1.522.7971939
X-RAY DIFFRACTIONr_mcangle_it2.2534.1882418
Refine LS restraints NCS

Ens-ID: 1 / Number: 14096 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 129 -
Rwork0.258 2141 -
all-2270 -
obs--94 %
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)
111.23120.11850.77632.3994-0.09962.70350.20860.5013-1.472-0.086-0.02380.27640.2511-0.27-0.18490.27590.0171-0.02990.1472-0.11530.54112.491-14.651-5.527
27.53211.2251.51586.6347-2.27187.30420.2364-0.2611-0.35160.4679-0.07640.24990.40090.1644-0.160.1470.06340.05230.1928-0.01320.2114-6.6782.8591.406
39.8442-2.40731.19074.053-0.93632.71420.0426-0.2023-0.73040.14370.0292-0.02270.12240.0106-0.07190.1879-0.01150.00470.1421-0.01790.21666.444-8.444-1.341
44.79581.4187-1.10083.6875-0.20843.80030.2745-0.39030.4830.6215-0.15320.05-0.179-0.071-0.12140.22550.01060.00220.215-0.02540.2322-2.51213.081.585
55.3260.8049-2.0193.2698-0.65494.04370.08030.4270.6176-0.29090.08540.1214-0.6443-0.0665-0.16570.21190.02560.0060.15770.03070.270121.48319.994-22.249
612.78551.3907-2.97135.3988-2.783113.1831-0.24790.19290.2442-0.0820.0946-0.72261.05150.12490.15330.5415-0.0496-0.01520.2969-0.09270.257925.0614.712-37.886
74.74560.8022-2.39442.4353-1.57727.5471-0.08840.11880.1139-0.25280.16210.15410.0828-0.3046-0.07370.07770.0362-0.01060.13110.03450.191319.18812.7-21.316
83.14490.4497-2.07716.01330.32536.2193-0.3980.4383-0.50350.17930.1435-0.15291.7964-0.60790.25461.0437-0.3225-0.03040.5769-0.04720.338917.6-4.604-37.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 114
2X-RAY DIFFRACTION2A115 - 138
3X-RAY DIFFRACTION3A139 - 193
4X-RAY DIFFRACTION4A194 - 296
5X-RAY DIFFRACTION5B44 - 116
6X-RAY DIFFRACTION6B117 - 140
7X-RAY DIFFRACTION7B141 - 195
8X-RAY DIFFRACTION8B196 - 291

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