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- PDB-3zwm: Crystal structure of ADP ribosyl cyclase complexed with substrate... -

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Basic information

Entry
Database: PDB / ID: 3zwm
TitleCrystal structure of ADP ribosyl cyclase complexed with substrate NAD and product cADPR
ComponentsADP-RIBOSYL CYLCASE
KeywordsHYDROLASE
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
CYCLIC ADENOSINE DIPHOSPHATE-RIBOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Dec 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)242,84016
Polymers237,7778
Non-polymers5,0638
Water5,314295
1
E: ADP-RIBOSYL CYLCASE
F: ADP-RIBOSYL CYLCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6494
Polymers59,4442
Non-polymers1,2052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area24240 Å2
MethodPISA
2
C: ADP-RIBOSYL CYLCASE
D: ADP-RIBOSYL CYLCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7714
Polymers59,4442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-17.3 kcal/mol
Surface area23940 Å2
MethodPISA
3
G: ADP-RIBOSYL CYLCASE
H: ADP-RIBOSYL CYLCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6494
Polymers59,4442
Non-polymers1,2052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-27.2 kcal/mol
Surface area24020 Å2
MethodPISA
4
A: ADP-RIBOSYL CYLCASE
B: ADP-RIBOSYL CYLCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7714
Polymers59,4442
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-20.6 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.578, 76.659, 140.325
Angle α, β, γ (deg.)87.78, 89.19, 89.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.614, -0.3075, -0.7269), (-0.3073, -0.9415, 0.1387), (-0.727, 0.1382, -0.6726)0.8474, 1.9952, 0.86
2given(0.9999, -0.01, 0.0126), (-0.0098, -0.9999, -0.0125), (0.0127, 0.0124, -0.9998)-28.1033, 36.691, -13.8603
3given(0.6044, 0.2909, 0.7417), (-0.3205, -0.108, -24.64), (-0.7294, -0.1724, 0.662)-17.4943, 0.9411, 36.6394
4given(0.5227, -0.7877, -0.3261), (-0.8447, -0.4269, -0.323), (0.1152, 0.4442, -0.8885)-18.9132, 37.6959, -84.1264
5given(0.5207, -0.6543, 0.5484), (0.6298, 0.7281, 0.2707), (-0.5764, 0.2044, 0.7912)37.1127, -39.5883, 76.8948
6given(0.5207, -0.6543, 0.5484), (0.6298, 0.7281, 0.2707), (-0.5764, 0.2044, 0.7912)37.1127, -39.5883, 76.8948
7given(0.5285, 0.7919, 0.3059), (-0.8417, 0.4416, 0.3107), (0.1109, -0.4217, 0.8999)-73.9601, 63.7493, 96.7499
8given(0.5279, 0.6354, -0.5636), (0.6208, -0.7415, -0.2546), (-0.5796, -0.2155, -0.7859)-135.0086, -17.3345, -2.577

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Components

#1: Protein
ADP-RIBOSYL CYLCASE / 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CXR / CYCLIC ADENOSINE DIPHOSPHATE-RIBOSE / CYCLIC ADP-RIBOSE


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 84316 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.3 / % possible all: 92.4

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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: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.607 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.631 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28453 4219 5 %RANDOM
Rwork0.21495 ---
obs0.21842 79952 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.945 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20.71 Å20.89 Å2
2---0.85 Å22.2 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16133 0 334 295 16762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.751.98623039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77852007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62823.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.915152796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5615112
X-RAY DIFFRACTIONr_chiral_restr0.1150.22441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112898
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_it0.6541.510075
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.282216247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19336878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5344.56792
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 266 -
Rwork0.3 5279 -
obs--86.36 %
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)
11.69580.1384-0.13521.1680.08331.2617-0.09280.11110.0968-0.3660.11370.1250.0183-0.0463-0.02090.2064-0.0817-0.05860.0851-0.03640.1019-5.5557-3.5955-13.1328
20.9758-0.16710.68991.1118-0.27581.2774-0.0027-0.15970.0308-0.04940.0529-0.0035-0.0623-0.0716-0.05010.0161-0.0298-0.00830.2034-0.0680.18088.21155.186213.3537
31.793-0.24630.00060.7722-0.23011.11960.0496-0.2232-0.04380.27540.10480.0505-0.0709-0.0868-0.15440.1260.0144-0.01420.1606-0.06070.158622.934439.95780.1401
41.17370.2852-0.24050.4888-0.04011.89420.02430.17890.0460.04680.0228-0.00180.0707-0.0548-0.04710.0379-0.0025-0.04230.1649-0.06640.210537.062131.8715-26.3238
50.7536-0.3414-0.57031.4837-0.98812.093-0.0581-0.02860.0919-0.0990.0819-0.07940.097-0.0502-0.02380.0384-0.0105-0.01040.1271-0.04540.163749.997738.5709-54.0713
61.1519-0.6229-0.0641.5635-1.16452.0844-0.00220.29440.1624-0.379-0.0297-0.08360.657-0.15340.03190.2439-0.03660.03920.15760.02870.054152.431435.676-84.92
70.710.18070.25121.7164-1.03012.0581-0.01370.039-0.11890.13830.14830.0014-0.1168-0.1615-0.13460.0232-0.0063-0.02180.1727-0.02750.146980.735770.7943-98.9859
80.9690.21550.13071.6892-1.40432.2147-0.1563-0.2667-0.13160.70110.2490.0067-0.9178-0.318-0.09270.4670.14670.03350.17130.04840.035183.071274.3575-68.1642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B-1 - 301
3X-RAY DIFFRACTION3C-1 - 301
4X-RAY DIFFRACTION4D0 - 301
5X-RAY DIFFRACTION5E-1 - 301
6X-RAY DIFFRACTION6F-1 - 303
7X-RAY DIFFRACTION7G1 - 301
8X-RAY DIFFRACTION8H-1 - 303

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