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- PDB-3dzf: Crystal structure of human CD38 extracellular domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3dzf
TitleCrystal structure of human CD38 extracellular domain complexed with a covalent intermediate, ara-F-ribose-5'-phosphate
ComponentsADP-ribosyl cyclase 1Cyclic ADP-ribose
KeywordsHYDROLASE / covalent intermediate / BETA SHEETS / ALPHA BUNDLE / Diabetes mellitus / Glycoprotein / Membrane / NAD / Receptor / Signal-anchor / Transmembrane
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 / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of bone resorption / response to hydroperoxide ...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 / 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 / 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 / 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
Chem-RF5 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 1.2Jun 8, 2016Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: ADP-ribosyl cyclase 1
F: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,67512
Polymers182,2826
Non-polymers1,3936
Water10,971609
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6122
Polymers30,3801
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.746, 96.156, 103.605
Angle α, β, γ (deg.)79.48, 82.72, 86.78
Int Tables number1
Space group name H-MP1

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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.: 6 / 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: Sugar
ChemComp-RF5 / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose / Inhibitor arabinosyl-2-fluoro-2-deoxynicotinamide mononucleotide, bound form / 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinose / 2-deoxy-2-fluoro-5-O-phosphono-D-arabinose / 2-deoxy-2-fluoro-5-O-phosphono-arabinose


Type: D-saccharide, alpha linking / Mass: 232.101 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10FO7P
IdentifierTypeProgram
a-D-Araf2fluoro5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM ...AUTHORS STATE THAT THE LIGAND RF5 IN THIS ENTRY IS A REACTION INTERMEDIATE, WITH THE (C1') ATOM HAVING SP2 HYBRIDIZATION (C1'H) NOT THE SP3 HYBRIDIZATION (C1'H2). AUTHORS ALSO STATE THAT THE PRESENCE OF COVALENT LINK IS THE NATURE OF THE COVALENT REACTION INTERMEDIATE RF5. THIS INTERMEDIATE IS NOT STABLE AND THEREFORE THE OUT-OF-RANGE COVALENT-BINDING DISTANCES REFLECT THE CHEMISTRY OF THIS INTERMEDIATE.

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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: 2.22 Å3/Da / Density % sol: 44.69 %
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 1, 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: 2→30 Å / Num. obs: 90177 / % possible obs: 86.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.485 / % possible all: 75

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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: 2.01→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.472 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 4493 5 %RANDOM
Rwork0.201 ---
obs0.205 85614 86.3 %-
all-85614 --
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: 38.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20.36 Å2-0.79 Å2
2---0.08 Å2-1.17 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12300 0 78 609 12987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02212720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.94117262
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93851506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80424.038624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.398152226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4641590
X-RAY DIFFRACTIONr_chiral_restr0.1360.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219606
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_it1.1511.57566
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.011212342
X-RAY DIFFRACTIONr_scbond_it3.2935154
X-RAY DIFFRACTIONr_scangle_it5.094.54920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 279 -
Rwork0.241 4984 -
obs--69.1 %
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)
12.52311.10130.75752.46621.40711.8246-0.00740.03580.4041-0.1515-0.02140.0023-0.1416-0.00770.0289-0.1760.02460.0289-0.19760.0172-0.1207-0.1860.807-0.91
22.73090.84450.52152.06771.17251.77360.03410.0110.248-0.1335-0.03550.011-0.0804-0.02280.0014-0.17150.02620.0214-0.21970.0262-0.1752-6.475-37.776-34.023
31.4181-0.0698-0.21281.3837-0.5243.06130.0604-0.3925-0.25160.34150.03120.01030.1558-0.0932-0.0917-0.0905-0.0343-0.0383-0.04270.0646-0.0678-22.543-26.75315.055
41.602-0.39450.30462.1355-1.13323.375-0.0192-0.5517-0.20290.44640.10140.10980.1059-0.1592-0.0823-0.0447-0.0240.00420.07170.0628-0.0299-29.342-7.231-52.888
52.10140.93590.71842.34751.61962.20730.01830.00930.1615-0.13750.0032-0.0561-0.12990.0018-0.0216-0.16430.00710.0375-0.1870.0093-0.128-7.1720.214-67.611
60.87760.2104-0.42591.1603-0.53023.50490.0552-0.2366-0.16150.267-0.00390.0150.203-0.0155-0.0512-0.0479-0.0129-0.0408-0.08380.0629-0.0277-23.79831.291-17.137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 2967 - 258
2X-RAY DIFFRACTION2BB45 - 2967 - 258
3X-RAY DIFFRACTION3CC45 - 2967 - 258
4X-RAY DIFFRACTION4DD45 - 2967 - 258
5X-RAY DIFFRACTION5EE45 - 2967 - 258
6X-RAY DIFFRACTION6FF45 - 2967 - 258

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