PDB-2o3u: Structural Basis for Formation and Hydrolysis of Calcium Messenge...

ID or keywords:

Entry

Database: PDB / ID: 2o3u

Title

Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38

Components

ADP-ribosyl cyclase 1

Keywords

HYDROLASE / Human CD38 E226Q mutant / the catalytic pocket / NGD binding and hydrolysis

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Liu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38
Authors: Liu, Q. / Kriksunov, I.A. / Graeff, R. / Lee, H.C. / Hao, Q.

History

Deposition	Dec 1, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 20, 2021	Group: Database references / Derived calculations / Structure summary Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2o3u.cif.gz	122.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2o3u.ent.gz	94.2 KB	Display	PDB format
PDBx/mmJSON format	2o3u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2o3u_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2o3u_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2o3u_validation.xml.gz	23.4 KB	Display
Data in CIF	2o3u_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o3/2o3u ftp://data.pdbj.org/pub/pdb/validation_reports/o3/2o3u	HTTPS FTP

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Related structure data

Related structure data	2o3qC 2o3rC 2o3sC 2o3tC 1yh3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3roq-2 3dzf-4 3dzi-2 4f45-2 3rok-2 2i66-2 3dzf-2 3rom-2 4jgj-d 3dzh-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (1)

Deposited unit

A: ADP-ribosyl cyclase 1

B: ADP-ribosyl cyclase 1

hetero molecules

62.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ADP-ribosyl cyclase 1

hetero molecules

defined by author
31.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ADP-ribosyl cyclase 1

hetero molecules

defined by author
31.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.975, 53.091, 65.678
Angle α, β, γ (deg.)	106.08, 91.92, 95.18
Int Tables number	1
Space group name H-M	P1

Details

There are two biological units in the crystallographic asymmetric unit.

#1: Protein	ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / ...Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / Lymphocyte differentiation antigen CD38 / T10 / Acute lymphoblastic leukemia cells antigen CD38 Mass: 30379.408 Da / Num. of mol.: 2 / Fragment: Extracellular domain, residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D, E226Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical	ChemComp-NGD / 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM / NICOTINAMIDE GUANINE DINUCLEOTIDE Mass: 680.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₅P₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.52 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 12% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2006
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. all: 30854 / Num. obs: 29497 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.1→2.18 Å / % possible all: 78.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ADSC	QUANTUM	data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1YH3

1yh3

Resolution: 2.11→20 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.931 / SU B: 10.08 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.251 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22268	1474	5 %	RANDOM
R_work	0.17791	-	-	-
all	0.18019	29500	-	-
obs	0.18019	27999	94.91 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 40.619 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.96 Å²	1.79 Å²	1.51 Å²
2-	-	1 Å²	2.14 Å²
3-	-	-	1.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.11→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4100	0	90	184	4374

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4312
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.398	1.96	5866
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.857	5	502
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.573	24.038	208
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.017	15	742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.316	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	628
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3250
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1854
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	2888
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	222
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.15	0.2	52
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.097	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.595	1.5	2591
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.95	2	4114
X-RAY DIFFRACTION	r_scbond_it	1.604	3	2002
X-RAY DIFFRACTION	r_scangle_it	2.526	4.5	1752
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.11→2.166 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.248	71	-
R_work	0.221	1452	-
obs	-	-	67.84 %

Refinement TLS params.

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

ID	L11 (°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)
1	0	0.007	-0.0134	31.0478	-59.3331	113.3869	1.264	0.2564	2.1398	-0.4662	-3.1112	-2.417	2.9016	1.0231	1.8471	0.3036	0.0439	-0.1485	0.4702	-0.0352	0.4283	23.5563	-17.3603	12.0229
2	9.8877	-2.9783	1.1627	3.9198	-1.3293	2.2684	0.2492	0.2689	-1.2286	-0.1815	0.055	0.5365	0.2583	-0.1816	-0.3042	-0.0971	0.0069	-0.0107	-0.2203	-0.0223	0.1806	0.7946	-14.972	-2.3705
3	3.818	-3.1428	-0.2508	5.7444	-0.0326	0.0346	0.2447	0.4062	-0.529	-0.4733	-0.1821	0.1571	0.0965	0.1551	-0.0626	-0.1252	-0.0048	0.0085	-0.0922	-0.0059	-0.1414	-2.7425	-1.71	-5.3805
4	17.8215	1.8234	1.2999	8.3491	1.8105	14.761	0.2492	-0.0496	-0.2491	0.0606	-0.1667	0.9517	0.4672	-0.7287	-0.0825	0.0196	-0.0283	0.0553	-0.153	0.0468	-0.1389	-12.6407	2.3211	5.8651
5	6.8931	-3.8581	0.8953	5.7361	-1.4025	2.0646	-0.0338	-0.3073	-0.3742	0.1999	0.0399	-0.3805	-0.0221	0.2634	-0.0062	-0.1644	-0.0082	0.004	-0.1667	0.0157	-0.0468	8.2211	-9.091	0.6023
6	4.8518	-0.5518	0.569	4.1947	-0.4073	6.1688	-0.0351	0.1888	-0.0408	0.2182	0.0349	-0.1795	0.0289	0.5021	0.0002	-0.2055	-0.0155	0.0032	-0.2103	0.016	-0.23	0.8069	9.6696	-2.4159
7	4.8018	0.715	-0.1987	5.1797	0.0508	5.1569	0.132	-0.5935	0.3973	0.8126	-0.0963	-0.142	-0.6623	-0.0959	-0.0357	-0.0357	-0.0172	-0.0418	-0.1185	-0.0339	-0.1563	-1.2979	18.9906	4.4376
8	19.4591	12.5232	-4.2008	21.0896	-5.9462	6.9884	0.465	-0.8056	1.276	0.8916	0.1914	1.5649	-0.5757	-1.3203	-0.6564	0.1607	0.0846	0.0895	0.167	-0.0424	-0.1665	-15.9625	12.374	14.3546
9	19.7759	-2.513	19.3214	14.92	22.4118	113.4597	-0.0859	-1.4059	0.376	0.9298	0.3866	-0.0024	-0.909	-2.6684	-0.3007	0.0741	0.1729	0.0147	0.1008	0.0451	-0.1828	24.6365	12.1708	4.2107
10	21.3914	4.1491	-7.3121	6.5528	-4.7801	11.3259	-0.0661	-0.1835	0.1712	0.1707	0.0433	-0.0124	0.0303	0.3108	0.0227	-0.223	0.0072	-0.0551	-0.2344	-0.0511	-0.3118	25.0302	13.9158	-10.7221
11	2.9363	0.5783	-1.5836	1.8786	-1.6003	6.515	0.1002	0.3976	0.2894	-0.1916	0.0227	0.0282	-0.6526	-0.1779	-0.1228	-0.0494	0.01	-0.0088	-0.1814	0.0146	-0.1475	19.277	22.9084	-25.4297
12	11.306	-2.2704	2.1427	4.2103	1.1295	10.4484	-0.0537	0.7076	0.067	-0.4694	-0.0122	-0.5714	-0.0258	0.8922	0.0659	-0.0399	-0.0439	0.0294	-0.0761	-0.1365	-0.125	24.7426	6.1903	-37.2461
13	3.9661	-0.3873	-1.4863	4.6835	2.6542	8.6942	-0.189	0.0691	-0.0901	-0.117	0.0405	0.1716	-0.0877	0.4712	0.1485	-0.2018	-0.0419	-0.0026	-0.2542	0.0038	-0.214	21.3866	16.2412	-23.5595
14	3.7993	0.1065	0.861	2.5533	0.7548	8.7744	0.1392	0.0953	-0.5675	0.0144	0.091	0.1844	0.2177	-0.3037	-0.2302	-0.2526	0.0006	-0.0022	-0.1956	-0.0271	-0.1488	16.2016	10.7942	-17.1519
15	4.2736	-0.1551	-0.5625	6.1583	0.3076	7.1842	-0.1958	0.1894	-0.9364	0.1701	-0.0488	0.3513	0.9616	-0.4466	0.2446	0.0738	-0.1339	0.008	0.0186	-0.1593	0.0194	15.0332	-4.0593	-35.813
16	16.0054	5.2031	-3.117	18.812	-1.2653	4.5443	-0.3179	1.4127	-1.1609	-1.8123	0.0465	-1.9856	0.8291	0.9452	0.2715	0.2724	0.155	0.1664	0.4859	-0.2269	0.19	33.2541	-3.8587	-44.734

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	45 - 49	7 - 11
2	X-RAY DIFFRACTION	2	A	A	50 - 103	12 - 65
3	X-RAY DIFFRACTION	3	A	A	104 - 129	66 - 91
4	X-RAY DIFFRACTION	4	A	A	130 - 143	92 - 105
5	X-RAY DIFFRACTION	5	A	A	144 - 193	106 - 155
6	X-RAY DIFFRACTION	6	A	A	194 - 235	156 - 197
7	X-RAY DIFFRACTION	7	A	A	236 - 275	198 - 237
8	X-RAY DIFFRACTION	8	A	A	276 - 296	238 - 258
9	X-RAY DIFFRACTION	9	B	B	45 - 48	7 - 10
10	X-RAY DIFFRACTION	10	B	B	49 - 58	11 - 20
11	X-RAY DIFFRACTION	11	B	B	59 - 116	21 - 78
12	X-RAY DIFFRACTION	12	B	B	117 - 140	79 - 102
13	X-RAY DIFFRACTION	13	B	B	141 - 167	103 - 129
14	X-RAY DIFFRACTION	14	B	B	168 - 195	130 - 157
15	X-RAY DIFFRACTION	15	B	B	196 - 275	158 - 237
16	X-RAY DIFFRACTION	16	B	B	276 - 296	238 - 258

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