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- PDB-6vua: X-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+ -

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Basic information

Entry
Database: PDB / ID: 6vua
TitleX-ray structure of human CD38 catalytic domain with 2'-Cl-araNAD+
ComponentsADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
KeywordsHYDROLASE / Inhibitor / CD38
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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Chem-ROJ / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDai, Z. / Zhang, X.N. / Nasertorabi, F. / Han, G.W. / Stevens, R.C. / Zhang, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
Other privateUniversity of Southern California Start-Up Fund for New Faculty and Sharon L. Cockrell Cancer Research Fund United States
Other privateThe V Foundation for Cancer Research V2016-021 United States
Other privateSTOP CANCER Research Career Development Award United States
Other privatePhRMA Foundation Research Starter Grant in Translational Medicine and Therapeutics United States
CitationJournal: Sci Adv / Year: 2020
Title: Synthesis of site-specific antibody-drug conjugates by ADP-ribosyl cyclases.
Authors: Dai, Z. / Zhang, X.N. / Nasertorabi, F. / Cheng, Q. / Li, J. / Katz, B.B. / Smbatyan, G. / Pei, H. / Louie, S.G. / Lenz, H.J. / Stevens, R.C. / Zhang, Y.
History
DepositionFeb 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Oct 23, 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

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)61,95417
Polymers59,5272
Non-polymers2,42715
Water9,044502
1
A: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9408
Polymers29,7641
Non-polymers1,1767
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)31,0149
Polymers29,7641
Non-polymers1,2518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.762, 114.762, 97.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-779-

HOH

31A-781-

HOH

41B-712-

HOH

51B-719-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 29763.738 Da / Num. of mol.: 2 / Mutation: N100D, N164A, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pFuse / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Strain (production host): Expi293
References: UniProt: P28907, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase

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Non-polymers , 7 types, 517 molecules

#2: Chemical ChemComp-ROJ / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R})-4-chloranyl-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate


Mass: 561.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22ClN5O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.73 Å3/Da / Density % sol: 55 %
Description: Large two dimensional, Thin, platelet like crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1) 100mM HEPES pH 7.0, 2) 38-42% Morpheus Precipitant mix 1 (MD2-250-84) containing PEG 1K, 3350 and MPD, 3) 100mM Potassium phosphate dibasic
PH range: 6.8-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→114.762 Å / Num. obs: 103758 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.091 / Rsym value: 0.088 / Net I/av σ(I): 4.1 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.5-1.5818.11.750.4149490.7480.421.8011.75100
1.58-1.6820.61.070.7141770.2421.0971.07100
1.68-1.7920.10.6611.2133700.1510.6780.661100
1.79-1.9419.20.3582.1124250.0840.3670.358100
1.94-2.1220.90.2023.6114870.0450.2070.202100
2.12-2.3720.40.1255.5104340.0290.1280.125100
2.37-2.7419.10.0887.492640.0210.0910.088100
2.74-3.3520.90.0639.578850.0140.0650.063100
3.35-4.7419.50.0561061890.0130.0580.056100
4.74-28.69118.60.0667.835780.0160.0680.06699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDR

6edr


Resolution: 1.5→28.71 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.692 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 5329 5.1 %RANDOM
Rwork0.1664 ---
obs0.1676 98376 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.85 Å2 / Biso mean: 30.512 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.96 Å2
Refinement stepCycle: final / Resolution: 1.5→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 151 512 4707
Biso mean--40.28 42.11 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174082
X-RAY DIFFRACTIONr_angle_refined_deg1.841.6516300
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5819531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56222.906234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2711525
X-RAY DIFFRACTIONr_chiral_restr0.350.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025086
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02957
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 385 -
Rwork0.284 7177 -
all-7562 -
obs--99.97 %
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)
10.18240.1223-0.07160.20880.10660.2591-0.0131-0.0054-0.0004-0.0005-0.00360.0251-0.00920.01410.01670.05540.00360.00290.05960.00210.0549-11.091-22.92611.486
20.8741-0.23470.03070.1293-0.030.00960.0309-0.0027-0.1472-0.0034-0.03230.0005-0.00380.01270.00140.01280.01070.00590.10090.00960.0755-49.858-15.48525.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 113
2X-RAY DIFFRACTION1A114 - 153
3X-RAY DIFFRACTION1A154 - 200
4X-RAY DIFFRACTION1A201 - 277
5X-RAY DIFFRACTION1A278 - 300
6X-RAY DIFFRACTION1A401
7X-RAY DIFFRACTION2B46 - 113
8X-RAY DIFFRACTION2B114 - 153
9X-RAY DIFFRACTION2B154 - 200
10X-RAY DIFFRACTION2B201 - 277
11X-RAY DIFFRACTION2B278 - 296
12X-RAY DIFFRACTION2B401

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