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- PDB-1zvm: Crystal structure of human CD38: cyclic-ADP-ribosyl synthetase/NA... -

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Basic information

Entry
Database: PDB / ID: 1zvm
TitleCrystal structure of human CD38: cyclic-ADP-ribosyl synthetase/NAD+ glycohydrolase
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE / NAD hydrolase / ADPR cyclase / dimer
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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NADP+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / 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 / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD metabolic process / NADP+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / 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 / response to estradiol / negative regulation of neuron projection development / 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
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsShi, W. / Yang, T. / Almo, S.C. / Schramm, V.L. / Sauve, A.
CitationJournal: To be Published
Title: Crystal structure of human CD38: Cyclic-ADP-ribosyl synthetase/NAD+ glycohydrolase
Authors: Shi, W. / Yang, T. / Almo, S.C. / Schramm, V.L. / Sauve, A.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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

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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
C: ADP-ribosyl cyclase 1
D: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,47512
Polymers118,7074
Non-polymers7698
Water4,017223
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8693
Polymers29,6771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8693
Polymers29,6771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8693
Polymers29,6771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8693
Polymers29,6771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: ADP-ribosyl cyclase 1
hetero molecules

C: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7386
Polymers59,3532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area2970 Å2
ΔGint-75 kcal/mol
Surface area24620 Å2
MethodPISA
6
D: ADP-ribosyl cyclase 1
hetero molecules

D: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7386
Polymers59,3532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2950 Å2
ΔGint-74 kcal/mol
Surface area24440 Å2
MethodPISA
7
A: ADP-ribosyl cyclase 1
hetero molecules

A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7386
Polymers59,3532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3060 Å2
ΔGint-74 kcal/mol
Surface area24030 Å2
MethodPISA
8
B: ADP-ribosyl cyclase 1
hetero molecules

B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7386
Polymers59,3532
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area3020 Å2
ΔGint-74 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.439, 115.704, 98.441
Angle α, β, γ (deg.)90, 90, 90
Int Tables number17
Space group name H-MP2221
Detailsdimer, not sure if it is present in the crystal stucture

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Components

#1: Protein
ADP-ribosyl cyclase 1 / Cyclic ADP-ribose / 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: 29676.660 Da / Num. of mol.: 4 / Mutation: N100D, N164A, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: the biologically significant dimer may not be present in the crystal structure
Gene: CD38 / Genus (production host): Pichia / Production host: Pichia (fungus) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / pH: 8.5
Details: PEG4000, Lithium sulfate, hexanediol, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2001
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 65067 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.3 / % possible all: 90.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→25 Å / Rfactor Rfree error: 0.004 / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5896 -RANDOM
Rwork0.228 ---
obs0.228 58229 86.8 %-
all-62325 --
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å20 Å2
2---3.69 Å20 Å2
3---8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8106 0 40 223 8369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.311 792 9.9 %
Rwork0.27 7194 -
obs--72.5 %

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