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

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Basic information

Entry
Database: PDB / ID: 3kou
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 / 2 GLYCOSIDASE / 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-2NF / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,7718
Polymers56,6022
Non-polymers2,1696
Water6,503361
1
A: CD38 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4874
Polymers28,3011
Non-polymers1,1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CD38 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2844
Polymers28,3011
Non-polymers9833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.721, 81.287, 150.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28301.045 Da / Num. of mol.: 2 / Fragment: UNP residues 32-278 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Strain: common european cow / References: UniProt: Q9TTF5, NAD+ glycohydrolase

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Sugars , 2 types, 2 molecules

#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 1
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

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Non-polymers , 3 types, 365 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H26FN7O13P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEG 4000, 50-250 mM ammonium sulfate, 100 mM Mes, pH 6-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6-6.5

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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 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: 1.78→75.4 Å / Num. obs: 52041 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 8
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6599 / Rsym value: 0.775 / % possible all: 82

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
ELVES-SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GH3

3gh3


Resolution: 1.78→40.644 Å / SU ML: 0.25 / Isotropic thermal model: 22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4018 7.78 %8% randomly selected reflections
Rwork0.1997 ---
obs0.203 51620 92.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.177 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0026 Å22.417 Å2-0.4144 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.78→40.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 104 361 4247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114026
X-RAY DIFFRACTIONf_angle_d1.2045449
X-RAY DIFFRACTIONf_dihedral_angle_d15.4921541
X-RAY DIFFRACTIONf_chiral_restr0.086576
X-RAY DIFFRACTIONf_plane_restr0.017699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80090.35091050.28141304X-RAY DIFFRACTION73
1.8009-1.82290.30741280.26241337X-RAY DIFFRACTION78
1.8229-1.8460.291220.24951434X-RAY DIFFRACTION82
1.846-1.87030.3091030.25121444X-RAY DIFFRACTION81
1.8703-1.89590.3141200.23971461X-RAY DIFFRACTION84
1.8959-1.9230.2731080.21331504X-RAY DIFFRACTION84
1.923-1.95170.26771190.23041510X-RAY DIFFRACTION84
1.9517-1.98220.24921270.2171472X-RAY DIFFRACTION86
1.9822-2.01470.25281510.21621568X-RAY DIFFRACTION89
2.0147-2.04940.25011280.21071523X-RAY DIFFRACTION87
2.0494-2.08670.26021530.21061586X-RAY DIFFRACTION90
2.0867-2.12680.25481470.21841626X-RAY DIFFRACTION92
2.1268-2.17020.24321490.20251614X-RAY DIFFRACTION92
2.1702-2.21740.25411460.20181664X-RAY DIFFRACTION94
2.2174-2.2690.26311380.18471633X-RAY DIFFRACTION94
2.269-2.32570.22791300.18221729X-RAY DIFFRACTION96
2.3257-2.38860.24231480.19011696X-RAY DIFFRACTION96
2.3886-2.45890.25161450.19321759X-RAY DIFFRACTION97
2.4589-2.53820.24771440.18081699X-RAY DIFFRACTION97
2.5382-2.62890.24011320.19951753X-RAY DIFFRACTION98
2.6289-2.73420.23811350.19171782X-RAY DIFFRACTION98
2.7342-2.85860.23681570.19891730X-RAY DIFFRACTION99
2.8586-3.00920.25751740.21081766X-RAY DIFFRACTION99
3.0092-3.19770.28251520.20191767X-RAY DIFFRACTION100
3.1977-3.44450.21681470.19111813X-RAY DIFFRACTION100
3.4445-3.79090.20181620.16891799X-RAY DIFFRACTION100
3.7909-4.33890.18521530.16061840X-RAY DIFFRACTION100
4.3389-5.46450.19091480.15551839X-RAY DIFFRACTION99
5.4645-40.65410.2231470.20241950X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.4720.3741-0.11290.96320.06780.1342-0.0255-0.0561-0.04960.00640.0257-0.0507-0.0135-0.016400.04310.01570.0010.03930.00630.06821.973542.03382.0077
20.9604-0.3229-0.63741.34920.30581.04630.08050.31330.031-0.2338-0.0235-0.0599-0.1133-0.02790.12930.0910.0036-0.0030.14660.01140.0226
Refinement TLS groupSelection details: chain B

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