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- PDB-3zwp: Crystal structure of ADP ribosyl cyclase complexed with ara-2'F-A... -

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Basic information

Entry
Database: PDB / ID: 3zwp
TitleCrystal structure of ADP ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.1 angstrom
ComponentsADP-RIBOSYL CYCLASE
KeywordsHYDROLASE / DP-RIBOSYL CYCLASE / CD38 / APLYSIA / BINDING SITES / HYDROLYSIS / NAD / PROTEIN CONFORMATION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NAD+ nucleosidase activity, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / positive regulation of B cell proliferation / transferase activity / cytoplasmic vesicle / 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-AVU / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKotaka, M. / Graeff, R. / Zhang, L.H. / Lee, H.C. / Hao, Q.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase.
Authors: Kotaka, M. / Graeff, R. / Chen, Z. / Zhang, L.H. / Lee, H.C. / Hao, Q.
History
DepositionAug 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
C: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
E: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
G: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,41619
Polymers237,7778
Non-polymers4,63911
Water20,1951121
1
A: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-7.2 kcal/mol
Surface area23660 Å2
MethodPISA
2
C: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7196
Polymers59,4442
Non-polymers1,2754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-8.7 kcal/mol
Surface area23380 Å2
MethodPISA
3
E: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6275
Polymers59,4442
Non-polymers1,1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-8.5 kcal/mol
Surface area23500 Å2
MethodPISA
4
G: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5354
Polymers59,4442
Non-polymers1,0912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-7.7 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.034, 77.610, 140.221
Angle α, β, γ (deg.)87.91, 89.24, 88.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6125, -0.3393, -0.7139), (-0.3342, -0.9297, 0.1551), (-0.7164, 0.1436, -0.6828)-0.1774, -0.2727, -0.1039
2given(0.9997, -0.0115, 0.022), (-0.0105, -0.9989, -0.0455), (0.0225, 0.0452, -0.9987)-29.1631, 34.8797, -15.3996
3given(0.597, 0.3007, 0.7437), (-0.3435, 0.9336, -0.1017), (-0.725, -0.1948, 0.6607)-18.8581, -24.2442, 37.0557
4given(0.5162, -0.7896, -0.3318), (-0.8454, -0.4075, -0.3454), (0.1374, 0.4588, -0.8778)-20.0993, 35.1299, -85.3151
5given(0.5202, -0.6591, 0.5431), (0.6209, 0.7285, 0.2894), (-0.5864, 0.1867, 0.7882)35.4719, -39.5634, 77.8737
6given(0.5293, 0.7947, 0.2973), (-0.8396, 0.4399, 0.3187), (0.1225, -0.4183, 0.9)-77.348, 63.8592, 95.6784
7given(0.5301, 0.629, -0.5686), (0.6118, -0.748, -0.2571), (-0.5871, -0.2116, -0.7814)-137.5432, -17.384, -1.2402

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Components

#1: Protein
ADP-RIBOSYL CYCLASE / ADRC / NAD GLYCOHYDROLASE / NAD(+) NUCLEOSIDASE / NADASE


Mass: 29722.102 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical
ChemComp-AVU / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / arabinosyl-2-fluoro-deoxy-adenosine diphosphate ribose, ara-2'F-ADPR


Mass: 545.307 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H22FN5O12P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE ADDITIONAL ALANINE RESIDUES AT THE N-TERMINUS ARE ACTUALLY LEFT OVER FROM THE CLEAVAGE OF THE ...THE ADDITIONAL ALANINE RESIDUES AT THE N-TERMINUS ARE ACTUALLY LEFT OVER FROM THE CLEAVAGE OF THE SECRETORY SIGNALLING PROTEIN FOR SECRETION DURING EXPRESSION FROM PICHIA.

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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: 2.9 Å3/Da / Density % sol: 57.62 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M IMIDAZOLE, PH 7.5, 12-14% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 141088 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R12

1r12


Resolution: 2.11→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.248 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24109 7090 5 %RANDOM
Rwork0.18543 ---
obs0.18822 133824 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0.06 Å20.4 Å2
2--0.49 Å20.51 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.11→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16116 0 298 1121 17535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02216899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.98122931
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80952004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06623.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.077152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.81715112
X-RAY DIFFRACTIONr_chiral_restr0.1390.22428
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112792
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_it1.1261.510052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.981216212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40236847
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.24.56719
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.105→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 421 -
Rwork0.239 7742 -
obs--74.36 %
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)
11.63110.1721-0.21020.6234-0.16790.6042-0.17040.25230.122-0.34060.20560.06630.147-0.0988-0.03520.3711-0.1369-0.0380.18820.03920.1591-6.7054-4.7948-12.7877
20.9120.04450.13110.6398-0.06890.5189-0.0595-0.11310.1141-0.06180.0462-0.01730.0103-0.03230.01330.1677-0.0195-0.00430.17680.00930.25397.1244.24512.8047
31.0806-0.2228-0.43180.6752-0.14150.5199-0.0378-0.09980.03080.24560.11220.0856-0.05820.0722-0.07430.25510.00040.00670.1806-0.03970.200322.530439.5706-0.1437
41.08110.0318-0.4760.5214-0.2221.3518-0.09010.2403-0.06960.0355-0.0293-0.04010.1159-0.04970.11940.1335-0.0459-0.00470.2592-0.04490.205737.121231.6613-26.1231
50.6853-0.2076-0.45990.6029-0.78152.3968-0.0959-0.09010.0867-0.10340.0016-0.08280.1683-0.00380.09430.1760.04650.0210.21830.00470.182450.506738.8996-53.9678
61.0026-0.432-0.19691.0801-0.61932.1874-0.09060.34460.0994-0.2293-0.00240.00910.6546-0.12170.0930.34530.00890.06570.2230.03110.103953.138836.1962-84.717
70.4670.32730.08791.1706-0.83071.225-0.0554-0.0391-0.07350.12060.20610.0064-0.1282-0.1494-0.15070.16080.04140.00030.23330.02480.212381.783871.4373-98.9433
81.3930.4008-0.07111.478-2.07513.2258-0.0821-0.3671-0.08970.81150.31620.1316-1.2836-0.4682-0.23410.68020.29420.07820.34140.04250.03383.940675.3513-68.2555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 252
2X-RAY DIFFRACTION2B1 - 252
3X-RAY DIFFRACTION3C1 - 252
4X-RAY DIFFRACTION4D1 - 252
5X-RAY DIFFRACTION5E1 - 252
6X-RAY DIFFRACTION6F1 - 252
7X-RAY DIFFRACTION7G1 - 252
8X-RAY DIFFRACTION8H1 - 252

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