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- PDB-8dsv: The structure of NicA2 in complex with N-methylmyosmine -

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Basic information

Entry
Database: PDB / ID: 8dsv
TitleThe structure of NicA2 in complex with N-methylmyosmine
ComponentsFAD-dependent oxidoreductase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / nicotine-degrading enzyme
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / N-methylmyosmine / FAD-dependent oxidoreductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, K. / Dulchavsky, M. / Li, J. / Bardwell, J.C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme.
Authors: Dulchavsky, M. / Mitra, R. / Wu, K. / Li, J. / Boer, K. / Liu, X. / Zhang, Z. / Vasquez, C. / Clark, C.T. / Funckes, K. / Shankar, K. / Bonnet-Zahedi, S. / Siddiq, M. / Sepulveda, Y. / ...Authors: Dulchavsky, M. / Mitra, R. / Wu, K. / Li, J. / Boer, K. / Liu, X. / Zhang, Z. / Vasquez, C. / Clark, C.T. / Funckes, K. / Shankar, K. / Bonnet-Zahedi, S. / Siddiq, M. / Sepulveda, Y. / Suhandynata, R.T. / Momper, J.D. / Calabrese, A.N. / George, O. / Stull, F. / Bardwell, J.C.A.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent oxidoreductase
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4658
Polymers95,2352
Non-polymers2,2306
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-18 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.080, 86.700, 152.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 51 through 136 or (resid 137...
d_2ens_1(chain "B" and (resid 51 through 95 or (resid 96...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASNA1 - 162
d_12ens_1TYRGLYA164 - 252
d_13ens_1VALSERA254 - 432
d_14ens_1FDAFDAB
d_21ens_1GLYASNE1 - 162
d_22ens_1TYRGLYE164 - 252
d_23ens_1VALSERE254 - 432
d_24ens_1FDAFDAF

NCS oper: (Code: givenMatrix: (0.0217184820196, 0.999247142448, 0.032147408099), (0.989680099887, -0.0260437787865, 0.140907847454), (0.141639003902, 0.0287553455072, -0.989500643092)Vector: 17. ...NCS oper: (Code: given
Matrix: (0.0217184820196, 0.999247142448, 0.032147408099), (0.989680099887, -0.0260437787865, 0.140907847454), (0.141639003902, 0.0287553455072, -0.989500643092)
Vector: 17.0895384055, -19.5081964375, 32.7370499834)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FAD-dependent oxidoreductase / Nicotine oxidoreductase / NicA2


Mass: 47617.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: A3L25_023855 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H5R8G3

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Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TXU / N-methylmyosmine


Mass: 160.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium citrate tribasic, pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→57.18 Å / Num. obs: 34120 / % possible obs: 97.2 % / Redundancy: 7 % / Biso Wilson estimate: 31.88 Å2 / CC1/2: 0.894 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 3430 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7C4A

7c4a


Resolution: 2.5→57.18 Å / SU ML: 0.2285 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2118 1688 4.96 %
Rwork0.1646 32368 -
obs0.1669 34056 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 2.5→57.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 151 264 7012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356911
X-RAY DIFFRACTIONf_angle_d0.64149392
X-RAY DIFFRACTIONf_chiral_restr0.04521031
X-RAY DIFFRACTIONf_plane_restr0.00551205
X-RAY DIFFRACTIONf_dihedral_angle_d11.4248965
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.20315417571 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.26051280.18732419X-RAY DIFFRACTION88.96
2.57-2.660.2511330.19032453X-RAY DIFFRACTION90.01
2.66-2.750.26551340.19612536X-RAY DIFFRACTION92.71
2.75-2.860.261350.20552617X-RAY DIFFRACTION96.09
2.86-2.990.24061370.20972719X-RAY DIFFRACTION97.91
2.99-3.150.22491340.19662723X-RAY DIFFRACTION99.03
3.15-3.350.25391310.18432771X-RAY DIFFRACTION99.79
3.35-3.610.22461590.16962771X-RAY DIFFRACTION100
3.61-3.970.19761420.14572792X-RAY DIFFRACTION100
3.97-4.540.14171380.12392786X-RAY DIFFRACTION99.97
4.54-5.720.17371530.12822827X-RAY DIFFRACTION100
5.72-57.180.21361640.16722954X-RAY DIFFRACTION99.65
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)
11.03620848292-0.503948794082-0.2151927964850.88804738063-0.3762620004610.402737056186-0.0359386922479-0.1079220168010.1835758118380.1414242889120.0124529684118-0.290839198336-0.04415794023890.1289207941920.009474232106980.177506424872-0.0366438138604-0.04398946648740.253540994236-0.01669168860660.23161856932821.5271588554-11.999754953524.0430770509
20.563939520943-0.556948439023-0.1911962498941.10394224595-0.002747789295170.548514296609-0.0631889634888-0.1547790072090.1245398180920.2615281301340.0666136855558-0.07219195198760.01801149974350.0620987552378-0.00680397806710.2386381554770.00136367845559-0.02669494126310.248701603665-0.01771780004230.1830089686088.56801389829-17.78481659332.1079495408
30.83458292553-1.17623245261-0.4721119500123.161275389470.03748910159530.500290775251-0.160982759812-0.1099247569020.07712728261170.4206059273160.125681383463-0.1952991800690.244953706479-0.0211263290730.04532065575990.226530043877-0.0131548039261-0.04469754640430.3279372570580.007490818196930.15412254161515.0392656635-30.021733610632.7931273258
41.78089317749-2.35396494313-1.699414480364.778684684251.568515246471.93076484634-0.237051090505-0.6835955103050.02236822040380.5201909180460.265376635044-0.460517016475-0.08303592546210.8209960212240.002873691219810.2902447559340.0134484013418-0.0518532385830.5087922804340.06613950898830.29839527216320.9770992165-38.176780902333.9660949434
50.930593084575-0.433424454136-0.02463337806881.82921603760.1911485370841.00192800712-0.0886073705107-0.2182032251740.191037540610.2288007651020.0401023681334-0.144282496081-0.1197166248570.02134822666290.05251831809520.224871853284-0.00828039898989-0.04443335405260.295436577898-0.04258292826580.24547656910114.3913977729-12.413317049334.1915294705
61.288003903030.118156768759-0.09746292363941.0442308884-0.2429701134221.23416872662-0.0693393413378-0.1476035242860.33935622323-0.0306863362346-0.00401631276547-0.0620515159598-0.3773195956040.07476977949780.05095246366170.286976044774-0.0264288560299-0.04653702624430.182416419847-0.01633724575920.2767691510135.56256080475.6813490701411.4948009049
74.53277560555-2.13143396024-0.1264669422725.29624361113-0.3256313080124.734748930130.0166681445953-0.328355479489-0.03328881628430.1910024247160.1579210066160.6002454202850.256677340083-0.35797022411-0.152105271040.165334314865-0.0562789401060.002895719449360.211602776331-0.03517522724770.251158821132-19.8670105553-13.18876632025.43445008872
88.50291967063-1.175920930381.505517116311.27786093112-0.6332984935680.4232558005740.2187892597330.312373611385-0.303073730637-0.316147294607-0.192398172040.03585235490430.02428307281110.0874700320569-0.04284661044310.234784238716-0.00512667677497-0.0127920702790.184522362238-0.05200305330090.1638335007140.749903025009-20.8647685935-1.27893082929
91.612134752480.7822928632920.8585255152710.9696452598770.4557612940381.3522327753-0.039615444356-0.09788435462260.106162866603-0.109345689242-0.01867140258410.0730034307083-0.103468965116-0.001403453913580.06033794913760.1878538693290.00982964961766-0.01037006391470.2054365763760.008947357255260.160096054889-6.83341415299-10.22775999784.83465438424
100.744321514578-0.327882201241-1.45281143952.204009896010.1581091302434.733726115740.108194508023-0.01026943428190.464222119664-0.2248917981710.0689056421873-0.254469024332-0.6471584758120.571257934337-0.2039982563380.354011099731-0.118987833418-0.0170235557270.2760786367530.02977003082880.40714514093416.093675608512.76557320143.09010324917
112.209008765150.787283196695-0.9266598789840.351743363865-0.568323853881.405321593240.009847179213360.3389868281220.4687622038990.06577818550470.0371267894297-0.169692424364-0.417660833048-0.000126078907583-0.05670411914880.484737034577-0.0992142268718-0.009299941825370.3366855139290.1181636440850.43212255099716.47072993729.20292014729-6.84146317538
125.42183208026-3.36875334078-1.481923670062.982850430181.569908157891.898300214920.1603406511960.4240413821620.0266266034989-0.213645888667-0.2685080367510.160767008013-0.361263772203-0.04683031129170.04853548031650.342397812645-0.0285856973217-0.02021503645770.1873201002880.06750154630560.255088385987-0.6099182882320.815245493593-5.34065703326
134.04082171132-1.19748739135-2.928177974441.873545707271.46015187287.231032740710.1385717479590.05292379426090.262350638455-0.0540125951398-0.04334309700260.302180488921-0.574475325412-0.287718707443-0.0889307906140.3141935320150.0142933262117-0.02692506890290.234201791432-0.001960246723980.352364043147-18.7785585733.550697189234.34167725469
140.796941324736-0.04567142458120.01185739904861.56366872608-0.01498871130551.30861416412-0.03400019961110.08759886935170.150200472442-0.121590951434-0.0377583345465-0.140988637386-0.1933528154170.1313755221550.07023257369680.262554400417-0.0325794902151-0.01139373974550.1976217070380.03337239958890.2477247922275.95202876918-0.2481059985040.778173957051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 51 through 136 )AA51 - 1361 - 86
22chain 'A' and (resid 137 through 323 )AA137 - 32387 - 273
33chain 'A' and (resid 324 through 371 )AA324 - 371274 - 321
44chain 'A' and (resid 372 through 403 )AA372 - 403322 - 353
55chain 'A' and (resid 404 through 482 )AA404 - 482354 - 432
66chain 'B' and (resid 51 through 136 )BE51 - 1361 - 86
77chain 'B' and (resid 137 through 166 )BE137 - 16687 - 116
88chain 'B' and (resid 167 through 204 )BE167 - 204117 - 154
99chain 'B' and (resid 205 through 257 )BE205 - 257155 - 207
1010chain 'B' and (resid 258 through 293 )BE258 - 293208 - 243
1111chain 'B' and (resid 294 through 323 )BE294 - 323244 - 273
1212chain 'B' and (resid 324 through 345 )BE324 - 345274 - 295
1313chain 'B' and (resid 346 through 403 )BE346 - 403296 - 353
1414chain 'B' and (resid 404 through 482 )BE404 - 482354 - 432

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