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- PDB-3raj: Crystal structure of human CD38 in complex with the Fab fragment ... -

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Basic information

Entry
Database: PDB / ID: 3raj
TitleCrystal structure of human CD38 in complex with the Fab fragment of antibody HB7
Components
  • ADP-ribosyl cyclase 1
  • heavy chain of the Fab fragment of antibody HB7
  • light chain of the Fab fragment of antibody HB7
KeywordsHYDROLASE/IMMUNE SYSTEM / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / agonistic antibody / HB7 / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / B cell proliferation / response to retinoic acid / positive regulation of vasoconstriction / positive regulation of B cell proliferation / response to interleukin-1 / response to progesterone / female pregnancy / B cell receptor signaling pathway / apoptotic signaling pathway / positive regulation of insulin secretion / response to estradiol / transferase activity / negative regulation of neuron projection development / positive regulation of cytosolic calcium ion concentration / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold ...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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.044 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: To be Published
Title: Engineering a novel cytosolic form of CD38 for cyclic ADP-ribose dependent signaling
Authors: Zhang, H. / Zhao, Y.J. / Hao, Q. / Lee, H.C.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
H: heavy chain of the Fab fragment of antibody HB7
L: light chain of the Fab fragment of antibody HB7


Theoretical massNumber of molelcules
Total (without water)76,6943
Polymers76,6943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.664, 271.521, 136.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 29812.738 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 46-300 / Mutation: Q49T, N100D, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Antibody heavy chain of the Fab fragment of antibody HB7


Mass: 23628.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse)
#3: Antibody light chain of the Fab fragment of antibody HB7


Mass: 23252.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse)
Has protein modificationY

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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: 3.61 Å3/Da / Density % sol: 65.91 % / Mosaicity: 1.003 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.6M sodium formate, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.044→50 Å / Num. obs: 19878 / % possible obs: 92.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.085 / Χ2: 2.323 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.164.50.44515421.09472.5
3.16-3.295.10.33517381.25382.4
3.29-3.435.50.26118521.5188.1
3.43-3.625.80.20519251.75390.5
3.62-3.845.80.15819842.06593.6
3.84-4.145.80.12620742.42896.9
4.14-4.565.70.10121312.83499.3
4.56-5.215.80.08421513.09999.8
5.21-6.575.70.08221923.09799.9
6.57-505.30.04422892.97899.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_378refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3


Resolution: 3.044→48.157 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7539 / SU ML: 0.38 / σ(F): 0.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 1001 5.06 %
Rwork0.2049 --
obs0.2084 19773 90.5 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 219.13 Å2 / Biso mean: 98.38 Å2 / Biso min: 20.73 Å2
Baniso -1Baniso -2Baniso -3
1-6.6805 Å2-0 Å20 Å2
2---10.4569 Å2-0 Å2
3---32.8916 Å2
Refinement stepCycle: LAST / Resolution: 3.044→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 0 0 5034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015164
X-RAY DIFFRACTIONf_angle_d1.3557015
X-RAY DIFFRACTIONf_chiral_restr0.087793
X-RAY DIFFRACTIONf_plane_restr0.006889
X-RAY DIFFRACTIONf_dihedral_angle_d16.5551833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0438-3.20420.3721020.28591956205867
3.2042-3.40490.36221390.27742455259484
3.4049-3.66780.31031440.23972628277290
3.6678-4.03670.28231530.19252752290594
4.0367-4.62040.2751590.17812908306798
4.6204-5.81960.24851450.18822977312299
5.8196-48.1630.24751590.20143096325599

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