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- PDB-3p5s: Structural insights into the catalytic mechanism of CD38: Evidenc... -

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Basic information

Entry
Database: PDB / ID: 3p5s
TitleStructural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex
ComponentsCD38 molecule
KeywordsHYDROLASE / CD38 / CYCLIC ADP RIBOSE / ECTO-ADP-RIBOSYL CYCLASE / GLYCOSIDASE
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / metabolic process / positive regulation of B cell proliferation / transferase activity / 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-AVU / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEgea, P.F. / Muller-Stauffler, H. / Kohn, I. / Cakou-Kefir, C. / Stroud, R.M. / Kellenberburger, E. / Schuber, F.
CitationJournal: Plos One / Year: 2012
Title: Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.
Authors: Egea, P.F. / Muller-Steffner, H. / Kuhn, I. / Cakir-Kiefer, C. / Oppenheimer, N.J. / Stroud, R.M. / Kellenberger, E. / Schuber, F.
History
DepositionOct 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD38 molecule
B: CD38 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8998
Polymers63,1742
Non-polymers1,7256
Water6,143341
1
A: CD38 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,5871
Non-polymers8633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CD38 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,5871
Non-polymers8633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.205, 80.029, 157.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CD38 molecule / Ecto-NAD+ glycohydrolase


Mass: 31587.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CD38 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9TTF5, NAD+ glycohydrolase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AVU / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / arabinosyl-2-fluoro-deoxy-adenosine diphosphate ribose, ara-2'F-ADPR


Mass: 545.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22FN5O12P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 4000, 50-250 mM AMMONIUM SULFATE, 100 MM SODIUM CACODYLATE OR SODIUM ACETATE OR MES AT PH-6.0-6.5, pH 6.0 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.0 6.5

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2007 / Details: could not see them
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.95→78.8 Å / Num. all: 110000 / Num. obs: 39086 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.084 / Net I/σ(I): 1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
PHASERphasing
PHENIXmodel building
ELVESrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GC6

3gc6


Resolution: 1.95→40.014 Å / SU ML: 0.29 / Cross valid method: random throughout, test set / σ(F): 0 / σ(I): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2902 7.73 %random
Rwork0.2053 ---
obs0.209 37543 86.15 %-
all-39086 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.574 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.467 Å20 Å20 Å2
2--1.5643 Å2-0 Å2
3---3.9028 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 108 341 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094025
X-RAY DIFFRACTIONf_angle_d1.1925458
X-RAY DIFFRACTIONf_dihedral_angle_d18.8881582
X-RAY DIFFRACTIONf_chiral_restr0.079586
X-RAY DIFFRACTIONf_plane_restr0.005699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.36332910.28713208X-RAY DIFFRACTION82
2.0197-2.10060.30032810.2533501X-RAY DIFFRACTION87
2.1006-2.19620.30922860.23623477X-RAY DIFFRACTION88
2.1962-2.3120.27692980.21613529X-RAY DIFFRACTION89
2.312-2.45680.28882590.20893513X-RAY DIFFRACTION88
2.4568-2.64640.25552990.19673441X-RAY DIFFRACTION86
2.6464-2.91270.27192690.20613471X-RAY DIFFRACTION86
2.9127-3.3340.23062930.20173380X-RAY DIFFRACTION84
3.334-4.19980.23162840.18233401X-RAY DIFFRACTION83
4.1998-40.02290.2133420.19383720X-RAY DIFFRACTION88

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