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- PDB-3dzj: Crystal structure of human CD38 extracellular domain E226Q mutant... -

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Basic information

Entry
Database: PDB / ID: 3dzj
TitleCrystal structure of human CD38 extracellular domain E226Q mutant, NMN complex
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / NMN complex / E226Q mutant / BETA SHEETS / ALPHA BUNDLE / Alternative splicing / Diabetes mellitus / Glycoprotein / Membrane / NAD / Polymorphism / Receptor / Signal-anchor / Transmembrane
Function / homology
Function and homology information


Nicotinate metabolism / NAD+ nucleosidase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NAD(P)+ nucleosidase activity / phosphorus-oxygen lyase activity / long-term synaptic depression / negative regulation of bone resorption ...Nicotinate metabolism / NAD+ nucleosidase activity / 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NAD(P)+ nucleosidase activity / phosphorus-oxygen lyase activity / long-term synaptic depression / negative regulation of bone resorption / NAD metabolic process / response to hydroperoxide / positive regulation of vasoconstriction / positive regulation of insulin secretion / positive regulation of B cell proliferation / response to interleukin-1 / secretory granule membrane / apoptotic signaling pathway / response to retinoic acid / response to progesterone / female pregnancy / B cell receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / negative regulation of neuron projection development / transferase activity / response to estradiol / basolateral plasma membrane / positive regulation of cell growth / response to hypoxia / response to drug / negative regulation of transcription, DNA-templated / positive regulation of transcription, DNA-templated / negative regulation of apoptotic process / signal transduction / cell surface / extracellular exosome / membrane / integral component of membrane / identical protein binding / plasma membrane / nucleus
ADP-ribosyl cyclase / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 / ADP-ribosyl cyclase (CD38/157)
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)61,3414
Polymers60,6712
Non-polymers6702
Water6,666370
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6712
Polymers30,3351
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6712
Polymers30,3351
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)41.858, 53.228, 65.670
Angle α, β, γ (deg.)106.11, 91.97, 95.03
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 30335.400 Da / Num. of mol.: 2 / Fragment: Enzymatic domain: UNP residues 45-300 / Mutation: Q49T, N100D, N164A, N209D, N219D, E226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZ(alpha)A / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 (Invitrogen) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Nicotinamide mononucleotide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.3 Å3/Da / Density % sol: 46.61 %
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: Feb 21, 2006
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: 1.9→30 Å / Num. obs: 41633 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 21.2
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.436 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3
Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.106 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2061 5 %RANDOM
Rwork0.185 ---
Obs0.188 38959 100 %-
All-38959 --
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: 33.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20.56 Å20.45 Å2
2--0.65 Å20.98 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 44 370 4424
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0190.0224168
r_bond_other_d
r_angle_refined_deg1.7721.9455654
r_angle_other_deg
r_dihedral_angle_1_deg6.395502
r_dihedral_angle_2_deg36.31623.958192
r_dihedral_angle_3_deg15.77915710
r_dihedral_angle_4_deg17.8261526
r_chiral_restr0.1290.2602
r_gen_planes_refined0.0080.023150
r_gen_planes_other
r_nbd_refined0.2280.21949
r_nbd_other
r_nbtor_refined0.3140.22826
r_nbtor_other
r_xyhbond_nbd_refined0.1630.2323
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.1520.237
r_symmetry_vdw_other
r_symmetry_hbond_refined0.1090.214
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.211.52569
r_mcbond_other
r_mcangle_it1.88924050
r_scbond_it2.97531844
r_scangle_it4.5374.51604
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 138 -
Rwork0.233 2566 -
Obs--100 %

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