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- PDB-4f45: Crystal structure of human CD38 E226Q mutant in complex with NAADP -

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Basic information

Entry
Database: PDB / ID: 4f45
TitleCrystal structure of human CD38 E226Q mutant in complex with NAADP
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / CD38 / ADP-ribosyl cyclase / NAADP / Calcium signaling
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to hydroperoxide / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / apoptotic signaling pathway / response to progesterone / female pregnancy / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / 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-DN4 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: MESSENGER / Year: 2013
Title: Crystal Structures of Human CD38 in Complex with NAADP and ADPRP
Authors: Zhang, H. / Graeff, R. / Lee, H.C. / Hao, Q.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1124
Polymers59,6242
Non-polymers1,4892
Water1,58588
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5562
Polymers29,8121
Non-polymers7441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5562
Polymers29,8121
Non-polymers7441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.694, 54.565, 63.420
Angle α, β, γ (deg.)109.670, 91.110, 93.680
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 29811.754 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-300 / Mutation: Q49T, N100D, N164A, N209D, N219D, E226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-DN4 / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / Nicotinic acid adenine dinucleotide phosphate


Mass: 744.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O18P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.27 Å3/Da / Density % sol: 45.86 % / Mosaicity: 0.744 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH 4.0, 12% PEG 20K, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MX225 / Detector: CCD / Date: Dec 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28795 / % possible obs: 94 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Χ2: 1.37 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.90.26623750.924177.8
2.18-2.263.10.21925631.141183.5
2.26-2.373.30.18128151.012191.5
2.37-2.493.50.14529391.047196.6
2.49-2.653.70.11630141.151198.2
2.65-2.853.90.10230191.196198.4
2.85-3.1440.07830031.302198.2
3.14-3.5940.06330341.621198.9
3.59-4.523.90.05430381.977199.2
4.52-503.80.04729951.888197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2415 / WRfactor Rwork: 0.1826 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8413 / SU B: 11.561 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2363 / SU Rfree: 0.1938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1448 5 %RANDOM
Rwork0.1707 ---
obs0.1735 28791 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 167.2 Å2 / Biso mean: 61.2542 Å2 / Biso min: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-0.96 Å21.34 Å2
2--2.16 Å20.97 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 96 88 4217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024251
X-RAY DIFFRACTIONr_bond_other_d0.0010.022917
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9645786
X-RAY DIFFRACTIONr_angle_other_deg0.853.0087004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8524.158202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8211526
X-RAY DIFFRACTIONr_chiral_restr0.1420.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 80 -
Rwork0.237 1577 -
all-1657 -
obs--73.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
15.86771.1464-1.86322.5708-1.10046.41220.1813-0.210.7658-0.0847-0.0666-0.027-0.61860.2732-0.11470.12580.01770.02750.07120.0160.1908-399.546-918.6389.387
23.09710.0953-3.6086.45985.097810.313-0.30170.72530.0617-0.24150.4693-0.27830.3638-0.3681-0.16750.1851-0.01420.01460.36160.15220.204-399.818-928.472-6.475
36.42931.1028-3.86741.3266-1.29469.98130.0547-0.39860.0275-0.1201-0.00330.04760.04650.0833-0.05140.05060.0331-0.01180.11750.05030.1077-402.179-925.7629.524
49.3174-0.6809-3.0866.5717-1.31278.847-0.89050.4838-0.29050.07030.60590.04581.5507-1.28070.28470.5151-0.2343-0.00150.3159-0.00690.0671-407.471-938.315-5.207
511.0310.4456-4.18138.2976-2.39966.3755-0.8269-0.0778-1.6677-0.1659-0.1275-0.55352.2961-0.29150.95441.0308-0.06660.19790.2488-0.07720.3229-400.771-946.951-9.429
616.2188-1.85281.80113.058-0.22884.49590.29650.6598-2.2073-0.0187-0.16050.46920.5048-0.1637-0.13610.2070.0056-0.04960.1163-0.12220.4015-418.185-954.22726.418
74.2514-0.7579-0.04776.31160.43941.11620.04170.3885-0.34220.22440.12520.19860.15350.1679-0.1670.06520.037-0.0230.35250.01880.0789-427.18-938.7528.117
813.5748-3.86381.84094.273-1.68472.665-0.1625-0.2901-1.13180.2290.19630.18570.13950.041-0.03370.1864-0.0219-0.00210.16990.01340.106-417.9-949.1129.537
94.2585-3.2404-0.39865.3111-0.97971.6809-0.00490.33960.20360.0041-0.0324-0.27810.06390.06840.03730.0554-0.0494-0.02110.25790.02730.0339-416.97-937.73426.187
106.3881.6509-3.10074.0632-0.73385.95140.374-0.47420.75210.6643-0.14520.1338-0.25130.1761-0.22870.1620.02320.00980.2135-0.03410.1219-424.395-924.60633.155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 106
2X-RAY DIFFRACTION2A107 - 140
3X-RAY DIFFRACTION3A141 - 193
4X-RAY DIFFRACTION4A194 - 243
5X-RAY DIFFRACTION5A244 - 291
6X-RAY DIFFRACTION6B45 - 107
7X-RAY DIFFRACTION7B108 - 138
8X-RAY DIFFRACTION8B139 - 176
9X-RAY DIFFRACTION9B177 - 210
10X-RAY DIFFRACTION10B211 - 296

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