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- PDB-2i66: Structural Basis for the Mechanistic Understanding Human CD38 Con... -

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Basic information

Entry
Database: PDB / ID: 2i66
TitleStructural Basis for the Mechanistic Understanding Human CD38 Controlled Multiple Catalysis
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / the catalytic pocket / reaction product / reaction intermediate
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-G1R / Chem-G2R / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural basis for the mechanistic understanding of human CD38-controlled multiple catalysis.
Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Munshi, C. / Lee, H.C. / Hao, Q.
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Het group G1R 301 A and G1R 302 A form a guanosine diphosphoribose dimer

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0466
Polymers60,7612
Non-polymers2,2854
Water7,999444
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5313
Polymers30,3801
Non-polymers1,1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5153
Polymers30,3801
Non-polymers1,1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.710, 52.812, 65.424
Angle α, β, γ (deg.)105.93, 91.80, 95.22
Int Tables number1
Space group name H-MP1
DetailsThere are two biological units in the crystallographic asymmetric unit.

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / ...Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / Acute lymphoblastic leukemia cells antigen CD38


Mass: 30380.393 Da / Num. of mol.: 2 / Mutation: Q49T, N100D, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-G1R / [(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5S)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE / GUANOSINE DIPHOSPHORIBOSE


Mass: 575.315 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O15P2
#3: Chemical ChemComp-G2R / [(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE / GUANOSINE DIPHOSPHORIBOSE INTERMEDIATE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 12% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 57966 / Num. obs: 56343 / % possible obs: 97.2 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8
Reflection shellResolution: 1.7→1.76 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3

1yh3


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.441 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22913 2857 5.1 %RANDOM
Rwork0.18224 ---
all0.2 55012 --
obs0.18468 53472 100 %-
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 mean: 40.807 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20.93 Å20.96 Å2
2--1.24 Å22.02 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 146 444 4690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9825963
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2324.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86915742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0491530
X-RAY DIFFRACTIONr_chiral_restr0.1240.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.22154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22951
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0851.52578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78824114
X-RAY DIFFRACTIONr_scbond_it2.8132089
X-RAY DIFFRACTIONr_scangle_it4.4684.51849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.705→1.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 186 -
Rwork0.225 3674 -
obs--100 %

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