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- PDB-2eg9: Crystal structure of the truncated extracellular domain of mouse CD38 -

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Basic information

Entry
Database: PDB / ID: 2eg9
TitleCrystal structure of the truncated extracellular domain of mouse CD38
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE / CELL SUEFACE ANTIGEN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Nicotinate metabolism / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / response to xenobiotic stimulus => GO:0009410 / artery smooth muscle contraction / NADP+ nucleosidase activity / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / hydrolase activity, acting on glycosyl bonds ...Nicotinate metabolism / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / response to xenobiotic stimulus => GO:0009410 / artery smooth muscle contraction / NADP+ nucleosidase activity / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / hydrolase activity, acting on glycosyl bonds / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / secretory granule membrane / response to progesterone / response to hormone / female pregnancy / B cell receptor signaling pathway / positive regulation of insulin secretion / response to estradiol / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / membrane => GO:0016020 / response to hypoxia / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / 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
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKukimoto-Niino, M. / Mishima, C. / Wakiyama, M. / Terada, T. / Shirouzu, M. / Hara-Yokoyama, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the truncated extracellular domain of mouse CD38
Authors: Kukimoto-Niino, M. / Mishima, C. / Wakiyama, M. / Terada, T. / Shirouzu, M. / Hara-Yokoyama, M. / Yokoyama, S.
History
DepositionFeb 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 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


Theoretical massNumber of molelcules
Total (without water)58,2972
Polymers58,2972
Non-polymers00
Water41423
1
A: ADP-ribosyl cyclase 1


Theoretical massNumber of molelcules
Total (without water)29,1481
Polymers29,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosyl cyclase 1


Theoretical massNumber of molelcules
Total (without water)29,1481
Polymers29,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.072, 176.815, 44.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose / CD38 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / NIM-R5 antigen / I-19


Mass: 29148.295 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 48-288) / Mutation: N104D, N124D, N213D, N223D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd38 / Plasmid: pAc-BiP / Cell line (production host): Schneider Line 2 (S2) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P56528, NAD+ glycohydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 1500, 0.2M NDSB-256, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11912 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.85275 % / Biso Wilson estimate: 48.5 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.614
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 5.21615 / Rsym value: 0.226 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DF1

2df1
PDB Unreleased entry


Resolution: 2.8→49.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1293616.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.34 1225 10.3 %RANDOM
Rwork0.263 ---
obs0.263 11873 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0287 Å2 / ksol: 0.345101 e/Å3
Displacement parametersBiso mean: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1--16.1 Å20 Å20 Å2
2---23.34 Å20 Å2
3---39.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 0 23 3412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 178 9.4 %
Rwork0.315 1709 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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