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

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Basic information

Entry
Database: PDB / ID: 3ghh
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
Chem-2NF / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsEgea, P.F. / Muller-Steffner, H. / Stroud, R.M. / Oppenheimer, N.J. / Kellenberger, 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
DepositionMar 3, 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
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.src_method / _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 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 27, 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)58,59510
Polymers56,6002
Non-polymers1,9958
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-54 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.399, 79.411, 156.297
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: 28300.061 Da / Num. of mol.: 2 / Fragment: UNP residues 32-278 / Mutation: E218Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CD38 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2NF / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(3-carbamoylpyridin-1-ium-1yl)- 3-fluoro-,4- hydroxyoxolan-2-yl]methyl phosphate / nicotinamide 2'-deoxy-2'-fluororibofuranosyl adenine dinucleotide


Mass: 665.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26FN7O13P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
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: May 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 41975 / Num. obs: 41975 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.0702 / Net I/σ(I): 11.2
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 4109 / Rsym value: 0.609 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHASERphasing
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3GC6 and 1YH3

3gc6

1yh3


Resolution: 1.94→35.399 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 3242 7.75 %random
Rwork0.2063 ---
obs0.209 41859 95.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.733 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--3.8941 Å20 Å20 Å2
2---0.6402 Å20 Å2
3---4.5343 Å2
Refinement stepCycle: LAST / Resolution: 1.94→35.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 125 264 4147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114015
X-RAY DIFFRACTIONf_angle_d1.6555442
X-RAY DIFFRACTIONf_dihedral_angle_d18.6321529
X-RAY DIFFRACTIONf_chiral_restr0.081581
X-RAY DIFFRACTIONf_plane_restr0.008695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.96390.2521250.23331456X-RAY DIFFRACTION85
1.9639-1.99460.29931400.22731664X-RAY DIFFRACTION96
1.9946-2.02730.30571470.22531653X-RAY DIFFRACTION96
2.0273-2.06220.24121420.21191680X-RAY DIFFRACTION97
2.0622-2.09970.24521430.2021674X-RAY DIFFRACTION97
2.0997-2.14010.27621480.20711693X-RAY DIFFRACTION97
2.1401-2.18380.24681310.20571697X-RAY DIFFRACTION97
2.1838-2.23130.27261340.20361683X-RAY DIFFRACTION96
2.2313-2.28320.23261360.20411665X-RAY DIFFRACTION96
2.2832-2.34020.26521260.19841709X-RAY DIFFRACTION96
2.3402-2.40350.27311420.21691684X-RAY DIFFRACTION96
2.4035-2.47420.25391520.19911679X-RAY DIFFRACTION96
2.4742-2.55410.25541320.1981683X-RAY DIFFRACTION95
2.5541-2.64530.26011390.20181656X-RAY DIFFRACTION95
2.6453-2.75120.26411170.20951705X-RAY DIFFRACTION95
2.7512-2.87630.24331470.22691655X-RAY DIFFRACTION94
2.8763-3.02790.28521330.21341654X-RAY DIFFRACTION94
3.0279-3.21750.21391450.20211676X-RAY DIFFRACTION95
3.2175-3.46570.24541420.20311677X-RAY DIFFRACTION94
3.4657-3.81410.20821460.18531712X-RAY DIFFRACTION95
3.8141-4.36520.20251440.1731684X-RAY DIFFRACTION94
4.3652-5.49640.19261610.17251739X-RAY DIFFRACTION96
5.4964-35.40450.22181700.21311839X-RAY DIFFRACTION96

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