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- PDB-5bnf: Apo structure of porcine CD38 -

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Basic information

Entry
Database: PDB / ID: 5bnf
TitleApo structure of porcine CD38
ComponentsUncharacterized protein
KeywordsHYDROLASE / ADP-hydrolase / ADP-cyclase / calcium signalling / cADPR
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NADP+ nucleosidase activity / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of B cell proliferation / transferase activity / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTing, K.Y. / Leung, C.P.F. / Graeff, R.M. / Lee, H.C. / Hao, Q. / Kotaka, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong
CitationJournal: Protein Sci. / Year: 2016
Title: Porcine CD38 exhibits prominent secondary NAD(+) cyclase activity.
Authors: Ting, K.Y. / Leung, C.F. / Graeff, R.M. / Lee, H.C. / Hao, Q. / Kotaka, M.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,8622
Polymers52,8622
Non-polymers00
Water3,657203
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,4311
Polymers26,4311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,4311
Polymers26,4311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.541, 103.856, 63.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein / porcine CD38


Mass: 26431.062 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CD38 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: F1S5D9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 4000, PEG 400, magnesium chloride, tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 21063 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.106 / Χ2: 0.826 / Net I/av σ(I): 17.319 / Net I/σ(I): 5.9 / Num. measured all: 141831
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.384.70.49420240.44698.8
2.38-2.486.90.41120910.478100
2.48-2.597.10.33120760.511100
2.59-2.737.10.28920410.591100
2.73-2.97.10.18921210.616100
2.9-3.127.10.14320860.767100
3.12-3.437.10.10320910.879100
3.43-3.9370.07921361.085100
3.93-4.956.90.07321511.2699.9
4.95-306.40.07222461.49699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1080 5.1 %Random selection
Rwork0.2071 19947 --
obs-21027 99.6 %-
Solvent computationBsol: 31.8771 Å2
Displacement parametersBiso max: 137.66 Å2 / Biso mean: 42.2651 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.615 Å20 Å20 Å2
2--0.185 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 0 203 3828
Biso mean---38.25 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it5.0634
X-RAY DIFFRACTIONc_scbond_it9.7038
X-RAY DIFFRACTIONc_mcangle_it6.9128
X-RAY DIFFRACTIONc_scangle_it12.01612
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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