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- PDB-3dzh: Crystal structure of human CD38 extracellular domain, GTP complex -

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Basic information

Entry
Database: PDB / ID: 3dzh
TitleCrystal structure of human CD38 extracellular domain, GTP complex
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE / GTP COMPLEX / BETA SHEETS / ALPHA BUNDLE / Diabetes mellitus / Glycoprotein / Membrane / NAD / Receptor / Signal-anchor / Transmembrane
Function / homology
Function and homology information


phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / negative regulation of bone resorption ...phosphorus-oxygen lyase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / Nicotinate metabolism / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / negative regulation of bone resorption / response to hydroperoxide / long-term synaptic depression / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / response to progesterone / female pregnancy / apoptotic signaling pathway / 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 / 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 / membrane / identical protein binding / 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
GUANOSINE-5'-TRIPHOSPHATE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Q. / Kriksunov, I.A. / Jiang, H. / Graeff, R. / Lin, H. / Lee, H.C. / Hao, Q.
CitationJournal: Chem.Biol. / Year: 2008
Title: Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38.
Authors: Liu, Q. / Kriksunov, I.A. / Jiang, H. / Graeff, R. / Lin, H. / Lee, H.C. / Hao, Q.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)61,8074
Polymers60,7612
Non-polymers1,0462
Water6,810378
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9042
Polymers30,3801
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9042
Polymers30,3801
Non-polymers5231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.679, 52.646, 65.235
Angle α, β, γ (deg.)106.14, 91.83, 95.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
22B

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 6 / Auth seq-ID: 45 - 296 / Label seq-ID: 7 - 258

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
222BB

NCS ensembles :
ID
1
2

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Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10 / CD38 antigen


Mass: 30380.393 Da / Num. of mol.: 2 / Fragment: Enzymatic domain: UNP residues 45-300 / Mutation: Q49T, N100D, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZ(alpha)A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 (Invitrogen) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 298 K / pH: 6
Details: 100 mM MES pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9778
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2007
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 65992 / % possible obs: 95.5 % / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 21.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.352 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3

1yh3


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.549 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3345 5.1 %RANDOM
Rwork0.176 ---
obs0.179 62631 100 %-
all-62631 --
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 mean: 29.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20.22 Å20.25 Å2
2--0.24 Å20.64 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 64 378 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0224281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4751.9545822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11824.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44515742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2241530
X-RAY DIFFRACTIONr_chiral_restr0.1770.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5461.52522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52524114
X-RAY DIFFRACTIONr_scbond_it3.89231759
X-RAY DIFFRACTIONr_scangle_it6.0424.51708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Number: 2050 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Aloose positional0.655
22Bloose thermal2.5410
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 197 -
Rwork0.207 3545 -
obs--100 %
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)
10.18410.9183-1.39564.5801-6.960810.579-0.0394-0.04810.1422-0.16170.0125-0.05890.62040.15110.02690.1280.0242-0.02590.1309-0.0290.112823.5315-17.199312.3964
24.5316-0.14580.13471.0639-0.4511.33470.07570.1536-0.4867-0.05720.02010.1640.1254-0.0993-0.0959-0.04490.0026-0.0111-0.1228-0.02050.13790.8724-14.7077-2.1939
33.1527-1.921-0.86123.71490.6030.39430.09620.2749-0.4115-0.1261-0.06330.00140.12660.032-0.033-0.0978-0.0012-0.0054-0.08560.0007-0.0662-2.7736-1.5312-5.1019
45.89841.0647-1.48273.01160.385.32620.0003-0.0387-0.29620.21520.03980.17290.2309-0.1741-0.0402-0.0694-0.0030.0208-0.11150.0286-0.106-12.69452.70616.213
53.1484-1.78990.52062.1713-0.81581.210.0072-0.0635-0.20240.0938-0.0332-0.0898-0.03120.17960.026-0.0923-0.0144-0.0004-0.1192-0.00460.00048.2239-8.76940.617
63.5457-0.0807-0.04862.3750.11623.48160.00630.0414-0.12730.1314-0.0014-0.21140.08490.2767-0.0049-0.1389-0.0122-0.0008-0.14620.0223-0.1390.76599.5361-2.26
72.2680.1977-0.19711.8399-0.30543.58730.1183-0.33150.19520.389-0.0356-0.0408-0.410.0245-0.0827-0.0516-0.01780.0006-0.086-0.0084-0.111-1.037618.94894.6634
85.76184.5054-0.90436.0258-0.14292.0010.1308-0.53720.45360.1941-0.05080.6888-0.3147-0.3198-0.080.06120.01760.04760.07080.0074-0.0768-15.638112.504614.711
92.5006-1.03362.47674.8674.915410.398-0.027-0.06810.26150.1919-0.08250.25080.0678-0.5250.1096-0.00340.00590.00650.00890.0307-0.034323.300811.97323.9849
108.11591.8396-2.62443.9586-2.1414.6708-0.0454-0.25580.06710.0281-0.0677-0.0033-0.04360.18410.1131-0.15310.0116-0.0166-0.1233-0.0004-0.202524.675413.9017-10.3355
112.08850.5592-1.18361.134-1.01373.39910.04630.22360.1322-0.1647-0.0292-0.0257-0.3347-0.021-0.0171-0.04880.01450.0004-0.11090.0093-0.117319.019722.7678-25.0932
126.2847-1.16841.14453.4765-0.30355.5833-0.02830.1704-0.0232-0.0260.0119-0.29130.07130.39760.0164-0.0301-0.0069-0.0042-0.0344-0.0754-0.094424.60996.0799-36.8029
132.5171-0.1276-0.81022.27941.33655.84970.0480.07780.0408-0.09640.0571-0.0066-0.13130.1487-0.1051-0.15060.0025-0.0032-0.15860.0174-0.147221.236316.1346-23.2222
142.63070.40930.36461.4948-0.18875.11970.06330.0031-0.326-0.04280.00580.07650.1988-0.2924-0.0691-0.16170.01570.0101-0.1301-0.0162-0.102915.867810.7606-16.7518
152.0568-0.0511-0.35833.18020.05131.9262-0.0568-0.1193-0.38490.14940.00440.13610.3179-0.07870.05240.0515-0.0466-0.00840.0507-0.0477-0.026215.1184-3.901-35.3429
164.69612.2801-1.84963.3551-0.80712.8495-0.14280.257-0.1912-0.4367-0.0607-0.51660.25460.37260.20350.13840.03880.020.2194-0.02620.18333.2945-3.7119-44.0497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 497 - 11
2X-RAY DIFFRACTION2AA50 - 10312 - 65
3X-RAY DIFFRACTION3AA104 - 12966 - 91
4X-RAY DIFFRACTION4AA130 - 14392 - 105
5X-RAY DIFFRACTION5AA144 - 193106 - 155
6X-RAY DIFFRACTION6AA194 - 235156 - 197
7X-RAY DIFFRACTION7AA236 - 275198 - 237
8X-RAY DIFFRACTION8AA276 - 296238 - 258
9X-RAY DIFFRACTION9BB45 - 487 - 10
10X-RAY DIFFRACTION10BB49 - 5811 - 20
11X-RAY DIFFRACTION11BB59 - 11621 - 78
12X-RAY DIFFRACTION12BB117 - 14079 - 102
13X-RAY DIFFRACTION13BB141 - 167103 - 129
14X-RAY DIFFRACTION14BB168 - 195130 - 157
15X-RAY DIFFRACTION15BB196 - 275158 - 237
16X-RAY DIFFRACTION16BB276 - 296238 - 258

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