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- PDB-4ogw: Structure of a human CD38 mutant complexed with NMN -

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Basic information

Entry
Database: PDB / ID: 4ogw
TitleStructure of a human CD38 mutant complexed with NMN
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / ADP-ribosyl cyclase
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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsShewchuk, L.M. / Preugschat, F. / Carter, L.H. / Boros, E.E. / Moyer, M.B. / Stewart, E.L. / Porter, D.J.T.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: A pre-steady state and steady state kinetic analysis of the N-ribosyl hydrolase activity of hCD157.
Authors: Preugschat, F. / Carter, L.H. / Boros, E.E. / Porter, D.J. / Stewart, E.L. / Shewchuk, L.M.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9982
Polymers29,6631
Non-polymers3351
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.341, 64.467, 73.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29662.609 Da / Num. of mol.: 1 / Fragment: CD38, UNP residues 46-300 / Mutation: N100D, N164D, N209D, N219D, E226Q
Source method: isolated from a genetically manipulated source
Details: Expressed with a FLAG-6xHis-Tev tag. Tag cleaved prior to crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Production host: Komagataella pastoris (fungus) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23% PEG3350, 0.1M Bis-Tris-Propane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 31, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→48.45 Å / Num. all: 15181 / Num. obs: 14373 / % possible obs: 99.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.8
Reflection shellResolution: 2.054→2.107 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 9.8 / Num. unique all: 990 / % possible all: 96.06

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3

1yh3


Resolution: 2.05→48.45 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.583 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.263 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26185 761 5 %RANDOM
Rwork0.19791 ---
all0.20092 15181 --
obs0.20092 14373 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 22 189 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222097
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.942866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00824.78794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10515343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.754158
X-RAY DIFFRACTIONr_chiral_restr0.070.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211614
X-RAY DIFFRACTIONr_mcbond_it0.3621.51276
X-RAY DIFFRACTIONr_mcangle_it0.69522078
X-RAY DIFFRACTIONr_scbond_it0.9433821
X-RAY DIFFRACTIONr_scangle_it1.5684.5788
LS refinement shellResolution: 2.054→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 58 -
Rwork0.198 990 -
obs-990 96.06 %

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