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- PDB-3dzg: Crystal structure of human CD38 extracellular domain, ara-F-ribos... -

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Basic information

Entry
Database: PDB / ID: 3dzg
TitleCrystal structure of human CD38 extracellular domain, ara-F-ribose-5'-phosphate/nicotinamide complex
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE / covalent intermediate complex / nicotinamide complex / BETA SHEETS / ALPHA BUNDLE / Diabetes mellitus / Glycoprotein / Membrane / NAD / Receptor / Signal-anchor / Transmembrane
Function / homology
Function and homology information


phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / response to hydroperoxide ...phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / response to hydroperoxide / negative regulation of bone resorption / long-term synaptic depression / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / 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 / 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 / membrane / identical protein binding / 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
NICOTINAMIDE / Chem-RF5 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, Q. / Kriksunov, I.A. / Jiang, H. / Graeff, R. / Lin, H. / Lee, H.C. / Hao, Q.
CitationJournal: Chem.Biol. / Year: 2008
Title: Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38.
Authors: Liu, Q. / Kriksunov, I.A. / Jiang, H. / Graeff, R. / Lin, H. / Lee, H.C. / Hao, Q.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 8, 2016Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)61,4696
Polymers60,7612
Non-polymers7084
Water8,431468
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7353
Polymers30,3801
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7353
Polymers30,3801
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.689, 52.812, 65.381
Angle α, β, γ (deg.)106.06, 91.95, 95.12
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30380.393 Da / Num. of mol.: 2 / Fragment: Enzymatic domain: UNP residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZ(alpha)A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 (Invitrogen) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Sugar ChemComp-RF5 / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose / Inhibitor arabinosyl-2-fluoro-2-deoxynicotinamide mononucleotide, bound form / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinose / 2-deoxy-2-fluoro-5-O-phosphono-D-arabinose / 2-deoxy-2-fluoro-5-O-phosphono-arabinose


Type: D-saccharide, alpha linking / Mass: 232.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10FO7P
IdentifierTypeProgram
a-D-Araf2fluoro5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM ...AUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM HAVING SP2 HYBRIDIZATION (C1'H) NOT THE SP3 HYBRIDIZATION (C1'H2). AUTHORS ALSO STATE THAT THE PRESENCE OF COVALENT LINK IS THE NATURE OF THE COVALENT REACTION INTERMEDIATE RF5.

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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: 45.65 %
Crystal growTemperature: 298 K / pH: 6
Details: 100 mM MES pH 6.0, 15% PEG 4000, 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: 0.9778
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2007
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 61988 / % possible obs: 96.3 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 17.5
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.189 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3
Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.285 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3138 5.1 %RANDOM
Rwork0.174 ---
obs0.176 58833 100 %-
all-58833 --
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: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20.51 Å20.49 Å2
2--0.34 Å20.94 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 44 468 4612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9455776
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80624.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21115742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.61530
X-RAY DIFFRACTIONr_chiral_restr0.1020.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22128
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22906
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.52562
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48324114
X-RAY DIFFRACTIONr_scbond_it2.41531913
X-RAY DIFFRACTIONr_scangle_it3.7774.51662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 177 -
Rwork0.179 3602 -
obs--100 %

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