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- PDB-3dzi: Crystal structure of human CD38 extracellular domain, ribose-5'-p... -

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Basic information

Entry
Database: PDB / ID: 3dzi
TitleCrystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / Noncovalent intermediate / GTP complex / R5P-GTP adduct / BETA SHEETS / ALPHA BUNDLE / Alternative splicing / Diabetes mellitus / Glycoprotein / Membrane / NAD / Polymorphism / Receptor / Signal-anchor / Transmembrane
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
GUANOSINE-5'-TRIPHOSPHATE / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / Chem-RGT / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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)62,2335
Polymers60,7612
Non-polymers1,4733
Water6,197344
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers30,3801
Non-polymers7351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1183
Polymers30,3801
Non-polymers7372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.669, 52.747, 65.133
Angle α, β, γ (deg.)106.09, 91.92, 95.27
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 / 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: Chemical ChemComp-RGT / 2-amino-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-9H-purin-6-yl 5-O-phosphono-beta-D-ribofuranoside / (Ribose-5'-phosphate)-(guanosine-5'-triphosphate)


Mass: 735.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O21P4
#3: Chemical ChemComp-N / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 214.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O7P
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAUTHORS STATE THAT THE LIGAND [N] IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM ...AUTHORS STATE THAT THE LIGAND [N] 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 LIGAND RGT THAT IS PRESENT IN THIS ENTRY IS ALSO AN UNSTABLE INTERMEDIATE AND THEREFORE THE DISTORTED LINKAGE BETWEEN RIBOSE-PHOSPHATE AND GTP MOIETIES REFLECTS THE CHEMISTRY OF THE REACTION.

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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: 2.23 Å3/Da / Density % sol: 44.74 %
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: May 6, 2006
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: 1.73→30 Å / Num. obs: 53519 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 25.8
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2 / Rsym value: 0.458 / % possible all: 82.2

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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

1yh3


Resolution: 1.73→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.06 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2691 5.1 %RANDOM
Rwork0.177 ---
obs0.179 50238 95.8 %-
all-50238 --
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: 40.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20.42 Å20.44 Å2
2--0.66 Å21.17 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 45 45 344 4534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.965862
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72324.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0615742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1081530
X-RAY DIFFRACTIONr_chiral_restr0.1050.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.22098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22927
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.52575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5324114
X-RAY DIFFRACTIONr_scbond_it2.53531992
X-RAY DIFFRACTIONr_scangle_it4.0464.51748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 176 -
Rwork0.238 3151 -
obs--82.41 %

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