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- PDB-4f46: Crystal structure of wild type human CD38 in complex with NAADP a... -

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Basic information

Entry
Database: PDB / ID: 4f46
TitleCrystal structure of wild type human CD38 in complex with NAADP and ADPRP
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 / Chem-DVN / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Nov 13, 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: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0094
Polymers59,6252
Non-polymers1,3842
Water7,062392
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4522
Polymers29,8131
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5572
Polymers29,8131
Non-polymers7441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.848, 53.683, 63.380
Angle α, β, γ (deg.)110.350, 91.420, 94.530
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: 29812.738 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-300 / Mutation: Q49T, N100D, N164A, N209D, N219D
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-DVN / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3
#3: 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.: 1 / Source method: obtained synthetically / Formula: C21H27N6O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.23 Å3/Da / Density % sol: 44.8 % / Mosaicity: 0.389 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH 4.0, 15% PEG 10K, 0.2M ammonium acetate, 3% isopropanol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97623 Å
DetectorType: MX225 / Detector: CCD / Date: Sep 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.69→100 Å / Num. obs: 53940 / % possible obs: 95 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.649 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.764.30.21339041.006168.5
1.76-1.835.10.18447551.103183.6
1.83-1.916.20.16656141.113199.2
1.91-2.027.30.14456651.281100
2.02-2.147.50.11956831.4171100
2.14-2.317.60.10156721.5151100
2.31-2.547.70.08956811.6591100
2.54-2.917.80.0856462.251100
2.91-3.6680.08256832.4791100
3.66-1007.80.06756371.779199.2

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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
Starting model: 1YH3

1yh3


Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2202 / WRfactor Rwork: 0.1852 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8856 / SU B: 3.825 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1084 / SU Rfree: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 2718 5 %RANDOM
Rwork0.1664 ---
obs0.1679 53915 94.14 %-
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: 80.07 Å2 / Biso mean: 31.0308 Å2 / Biso min: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0.06 Å20.08 Å2
2--0.4 Å20.45 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 66 392 4516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024268
X-RAY DIFFRACTIONr_bond_other_d0.0020.022935
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9545812
X-RAY DIFFRACTIONr_angle_other_deg0.8673.0127117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89624.272206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03315734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6691526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 127 -
Rwork0.225 2304 -
all-2431 -
obs--57.15 %
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)
12.13520.1249-0.55861.6905-1.24393.54170.0538-0.02080.161-0.0347-0.0462-0.0721-0.2150.1096-0.00750.09970.00590.00170.0232-0.01780.0728-399.8-918.4318.491
26.8586-0.24981.99585.2371-1.27995.8814-0.11990.2539-0.10740.0599-0.0307-0.56350.06220.44610.15050.1404-0.02040.0030.1157-0.05050.1306-396.099-932.806-7.713
33.08330.4185-0.62261.3035-0.31246.1528-0.0413-0.1261-0.1232-0.0361-0.00960.02770.1495-0.1020.0510.02720.0114-0.01020.01680.00690.0536-401.522-926.0379.723
45.7006-0.7587-0.2044.5937-0.1173.2814-0.2063-0.3467-0.30740.35820.16390.1420.1486-0.27380.04230.1614-0.04960.01050.1252-0.02050.1027-407.347-937.138-3.74
55.1397-2.59570.16662.45640.04051.1442-0.06520.136-0.2202-0.0232-0.0251-0.00740.17190.05320.09040.2484-0.02270.04130.1512-0.04970.1699-400.044-945.76-10.227
63.8285-1.47050.19352.4726-0.00570.46970.20850.224-1.0172-0.0719-0.08460.16670.14960.0465-0.1240.1490.0064-0.05890.1597-0.03030.3474-418.427-952.34124.609
77.6763.8184-3.3928.60640.19216.24320.1147-0.3938-0.04980.7379-0.13910.48130.2746-0.18470.02430.17210.01960.02980.07360.03350.0873-428.163-937.42433.962
813.8985-1.62111.53581.4839-1.13282.01840.2455-0.247-1.33170.0693-0.1834-0.09130.1060.335-0.0620.1378-0.0059-0.06540.11710.06230.2752-411.478-951.57229.268
98.8212-7.63131.95267.7281-2.16571.29820.25910.4647-0.145-0.2624-0.2859-0.03740.10770.17740.02690.0654-0.00580.00280.0865-0.00240.0592-416.371-940.11722.525
102.5739-0.1327-1.6132.16120.07493.91320.0234-0.25910.11880.31170.0160.057-0.15750.1159-0.03940.1292-0.0045-0.00210.1006-0.00090.0591-424.079-925.09333.62
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 116
2X-RAY DIFFRACTION2A117 - 140
3X-RAY DIFFRACTION3A141 - 193
4X-RAY DIFFRACTION4A194 - 233
5X-RAY DIFFRACTION5A234 - 291
6X-RAY DIFFRACTION6B45 - 123
7X-RAY DIFFRACTION7B124 - 145
8X-RAY DIFFRACTION8B146 - 178
9X-RAY DIFFRACTION9B179 - 203
10X-RAY DIFFRACTION10B204 - 296

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