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- PDB-3gh3: Structural insights into the catalytic mechanism of CD38: Evidenc... -

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Basic information

Entry
Database: PDB / ID: 3gh3
TitleStructural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex.
ComponentsEcto-NAD+ glycohydrolase (CD38 molecule)
KeywordsHYDROLASE / CD38 / CYCLIC ADP RIBOSE / ECTO-ADP-RIBOSYL CYCLASE / 2 GLYCOSIDASE / Glycosidase
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / transferase activity / 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
CACODYLATE ION / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEgea, P.F. / Muller-Steffner, H. / Stroud, R.M. / Kellenberger, E. / Oppenheimer, N. / 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
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ecto-NAD+ glycohydrolase (CD38 molecule)
B: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7807
Polymers56,6022
Non-polymers1,1785
Water9,512528
1
A: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8223
Polymers28,3011
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ecto-NAD+ glycohydrolase (CD38 molecule)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9584
Polymers28,3011
Non-polymers6573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.483, 80.879, 151.790
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 Ecto-NAD+ glycohydrolase (CD38 molecule)


Mass: 28301.045 Da / Num. of mol.: 2 / Fragment: UNP residues 32-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CD38, CD38 gene from Bos taurus / Production host: Pichia pastoris (fungus) / References: UniProt: Q9TTF5, NAD+ glycohydrolase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-30% PEG 4000, 50-250MM AMMONIUM SULFATE, 100 MM SODIUM CACODYLATE OR SODIUM ACETATE OR MES AT PH-6.0-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 53100 / Num. obs: 53100 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.034 / Net I/σ(I): 26
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.91 / Rsym value: 0.306 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHENIXPHASERmodel building
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GC6

3gc6


Resolution: 1.8→40.44 Å / SU ML: 0.22 / σ(F): 1 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 3873 7.58 %
Rwork0.1766 --
obs0.1802 51064 92.8 %
all-51067 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.715 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.07 Å20 Å20 Å2
2---7.9177 Å20 Å2
3----5.1526 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 71 528 4430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084071
X-RAY DIFFRACTIONf_angle_d1.1245540
X-RAY DIFFRACTIONf_dihedral_angle_d18.5311550
X-RAY DIFFRACTIONf_chiral_restr0.081602
X-RAY DIFFRACTIONf_plane_restr0.005713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82310.25711000.20021238X-RAY DIFFRACTION69
1.8231-1.84610.24911070.19581396X-RAY DIFFRACTION78
1.8461-1.87040.24131100.20311410X-RAY DIFFRACTION79
1.8704-1.89610.24261030.18921421X-RAY DIFFRACTION78
1.8961-1.92310.25531340.19311558X-RAY DIFFRACTION88
1.9231-1.95190.25351520.18571622X-RAY DIFFRACTION92
1.9519-1.98240.23951260.18241564X-RAY DIFFRACTION86
1.9824-2.01480.23871240.18171595X-RAY DIFFRACTION90
2.0148-2.04960.21481420.17851684X-RAY DIFFRACTION93
2.0496-2.08690.24291410.18111673X-RAY DIFFRACTION94
2.0869-2.1270.2251380.17761691X-RAY DIFFRACTION94
2.127-2.17040.26451390.17651687X-RAY DIFFRACTION94
2.1704-2.21760.24711230.17961685X-RAY DIFFRACTION94
2.2176-2.26920.26791580.1831785X-RAY DIFFRACTION98
2.2692-2.32590.23371530.17751639X-RAY DIFFRACTION93
2.3259-2.38880.23141550.17051719X-RAY DIFFRACTION95
2.3888-2.45910.22561320.17551749X-RAY DIFFRACTION97
2.4591-2.53840.22971600.1781770X-RAY DIFFRACTION98
2.5384-2.62920.22661460.18151760X-RAY DIFFRACTION98
2.6292-2.73440.22051690.17981766X-RAY DIFFRACTION98
2.7344-2.85880.23421350.17981798X-RAY DIFFRACTION99
2.8588-3.00950.21131660.17911784X-RAY DIFFRACTION98
3.0095-3.1980.23611280.17351834X-RAY DIFFRACTION99
3.198-3.44480.21251580.17281817X-RAY DIFFRACTION99
3.4448-3.79120.20571310.15261849X-RAY DIFFRACTION99
3.7912-4.33930.17341370.14221868X-RAY DIFFRACTION99
4.3393-5.46490.18181520.14581874X-RAY DIFFRACTION100
5.4649-40.44970.2071540.1891955X-RAY DIFFRACTION98

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