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- PDB-7u6l: Pseudooxynicotine amine oxidase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7u6l
TitlePseudooxynicotine amine oxidase
ComponentsAmine oxidase
KeywordsFLAVOPROTEIN / oxidoreductase / monoamine oxidase
Function / homology
Function and homology information


pseudooxynicotine dehydrogenase / nicotine catabolic process / alkaloid metabolic process / periplasmic space / oxidoreductase activity
Similarity search - Function
: / Flavin amine oxidase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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
FLAVIN-ADENINE DINUCLEOTIDE / Pseudooxynicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida S16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChoudhary, V. / Stull, F. / Wu, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM139069-01A1 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The enzyme pseudooxynicotine amine oxidase from Pseudomonas putida S16 is not an oxidase, but a dehydrogenase.
Authors: Choudhary, V. / Wu, K. / Zhang, Z. / Dulchavsky, M. / Barkman, T. / Bardwell, J.C.A. / Stull, F.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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: Amine oxidase
B: Amine oxidase
C: Amine oxidase
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,2288
Polymers201,0864
Non-polymers3,1424
Water6,738374
1
A: Amine oxidase
hetero molecules

D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1144
Polymers100,5432
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
2
B: Amine oxidase
C: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1144
Polymers100,5432
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.990, 50.340, 150.890
Angle α, β, γ (deg.)90.000, 107.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 13 through 57 or (resid 58...
d_2ens_1(chain "B" and (resid 13 through 57 or (resid 58...
d_3ens_1(chain "C" and (resid 13 through 97 or (resid 98...
d_4ens_1(chain "D" and (resid 13 through 58 or resid 62...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALLEUA1 - 46
d_12ens_1LYSGLUA48 - 434
d_13ens_1FADFADB
d_21ens_1VALLEUC1 - 46
d_22ens_1LYSGLUC49 - 435
d_23ens_1FADFADD
d_31ens_1VALGLUE1 - 433
d_32ens_1FADFADF
d_41ens_1VALLEUG1 - 46
d_42ens_1LYSGLUG49 - 435
d_43ens_1FADFADH

NCS oper:
IDCodeMatrixVector
1given(0.00886625712259, -0.480459597138, -0.876972043456), (0.49286692614, 0.765177586509, -0.414228746252), (0.870059528195, -0.428557856796, 0.243586906002)-12.9750141798, -57.3125643263, -1.84022030682
2given(0.997527047724, -0.0118074764903, 0.0692847209586), (-0.0131110748699, -0.99974491032, 0.0183905955736), (0.0690499006164, -0.0192535136723, -0.997427397576)-40.2472557612, -7.99404034526, 1.99639507074
3given(-0.0916828954446, 0.516254245784, 0.851513828656), (-0.495149650306, -0.765542249806, 0.410818557959), (0.863956636924, -0.383961739594, 0.325810239316)-26.1818585566, 23.0149548002, -4.90027379135

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Components

#1: Protein
Amine oxidase


Mass: 50271.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida S16 (bacteria) / Strain: S16 / Gene: PPS_4080
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F8G0P1
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystal condition: 0.18M Potassium Bromide + 29% PEG 4000 + 0.1M TAPS pH 9
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. obs: 64436 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.87 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.66 Å / CC1/2: 0.982 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c71

6c71


Resolution: 2.6→47.99 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 19.9444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 1969 3.12 %
Rwork0.1701 61107 -
obs0.1717 63076 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13399 0 212 374 13985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004113945
X-RAY DIFFRACTIONf_angle_d0.744719020
X-RAY DIFFRACTIONf_chiral_restr0.04882110
X-RAY DIFFRACTIONf_plane_restr0.00582423
X-RAY DIFFRACTIONf_dihedral_angle_d11.16671897
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.518460162464
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.497974186017
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.513447996317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.30691450.22464225X-RAY DIFFRACTION95.19
2.67-2.740.24971200.20694211X-RAY DIFFRACTION95.92
2.74-2.820.28341540.19064227X-RAY DIFFRACTION95.99
2.82-2.910.25611300.18464258X-RAY DIFFRACTION96.52
2.91-3.010.20831470.17634294X-RAY DIFFRACTION97.3
3.01-3.130.2531300.17814350X-RAY DIFFRACTION97.62
3.13-3.280.24471400.17414316X-RAY DIFFRACTION98.08
3.28-3.450.21721320.16394371X-RAY DIFFRACTION98.73
3.45-3.660.20871420.17034386X-RAY DIFFRACTION98.74
3.66-3.950.23231410.16644430X-RAY DIFFRACTION99.18
3.95-4.340.20441460.14884433X-RAY DIFFRACTION99.26
4.34-4.970.16981450.14384486X-RAY DIFFRACTION99.55
4.97-6.260.19191430.17564492X-RAY DIFFRACTION99.14
6.26-47.990.20321540.1654628X-RAY DIFFRACTION99.25
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)
10.917002928699-0.708902369585-0.08735434541972.00918475811-0.9219411054881.804792334370.0259712141322-0.4904411759110.1907658864930.1558597541170.0729643421731-0.0401462790317-0.547257656403-0.139935736286-0.09716870700030.273807545353-0.02045154393430.02266042815650.335741063575-0.04088030299420.14667552978949.74892399868.95104159104-6.92577918847
22.56644870774-0.9512499221390.333315352591.16831747306-0.1197502113531.026914591770.1578168560980.2066762003420.000715472866332-0.114830731088-0.0870167498069-0.1594862285090.1032421338410.26915803991-0.06756647711960.2131113988690.005730580180290.03386899193690.2353677568050.01521975131610.16964738851767.59742717590.862750505658-27.1803407677
32.344328400990.3448822812870.2114146869491.828078881560.2153578597781.577789817290.1249656928480.0308122042307-0.732797696797-0.105196118802-0.000751358402078-0.2498855393360.3874487798230.239655967552-0.1214308430630.280925403780.0669340667388-0.03864543493940.20104068416-0.05367013081590.34085953371170.9402217118-14.0037570182-24.5796685388
41.88239559989-0.291364778858-0.06047964393431.16470421093-0.1976423466691.336584781470.0481779717761-0.0485023492966-0.1261851667630.0891607410859-0.08055023632470.0500160073541-0.0356421440017-0.04408138530190.03294163918120.181490368764-0.0488334105871-0.01399327683720.135340092455-0.03349060275640.16448482325958.59935261672.4525491459-16.3488114323
54.16005917774-0.798661365784-2.065937295892.029051388710.2190727708032.115478036240.165506869598-0.3626437407730.01856431051790.288506865317-0.129483215184-0.0500105212208-0.0526393760617-0.374460130663-0.01665769954950.251733803570.01789851656390.06738432406970.4740281835370.08098786390150.23117481635540.5779453904-0.4709224774461.43021095256
64.682923046820.872208799806-0.5533360790920.2332213762270.4244693721921.47042659311-0.116522949073-0.2434467587980.09359349212730.0935681465570.1507694937320.1658338387080.102209185224-0.0243182742993-0.007745526503020.2331643857080.0384732922733-0.02245682728470.3069915286930.07462748495530.25061383636258.7104765762-6.15318912965-5.25528537253
73.111894783710.28585822529-0.314860777830.91911497784-0.4582062184282.836240946050.004560396766640.013146937380.3119183665820.05318893877260.09984135101680.0961846580279-0.1686210582730.450928373897-0.09452001594020.163448544424-0.0491155036752-0.03401712331420.2598681512260.02078425081680.26091079288379.80259680464.64354767216-14.6232957041
81.7189496698-0.321187861687-0.2928655902360.549167473425-0.1827498324221.434672891330.0302553884205-0.387114528479-0.08994284782810.0226861978716-0.0116821831829-0.1137044932480.17232532436-0.0285925248648-0.001547877367250.197998147703-0.0110877746429-0.03896530177280.1408322684650.01044869976930.23549571027663.6583570895-2.29324240505-10.7506757735
97.28970988441.22297991334-2.858729473792.99006106565-0.5005081690662.651503962640.01366169661030.516195413673-0.5563047068360.0263874699219-0.05827921007930.1434830084760.0281041362972-0.6619316970870.07405821986050.16289373101-0.04329700941410.01435512407050.3051600044190.02454020555260.16478013104841.79744287280.91541106546-15.8148922896
101.214277351720.1280731584340.6367122771911.039126837410.4399822904252.032913154790.01359796120060.004424446781340.1373354496050.094797921197-0.07370924399840.271366376253-0.0494016848007-0.1488489493090.06948996066990.22440311542-0.003671085196750.07066932490880.1165928041210.008644797416970.242675248528-3.58506783357-16.039489227340.7729736262
111.26076218352-0.03112600429750.06991471459680.9868240581250.317097917860.6846119057690.00726367763595-0.244669949419-0.1734109384830.2110597888410.0540599169307-0.09934790576190.02712624052990.102169419733-0.05548533900890.2434720838320.009048107952070.002517262397710.1779952144080.04245360957070.2107598415989.72028484825-19.48281157451.1232662612
124.630309251382.235998408583.035805245583.56553494626-0.3296696303773.31534904041-0.02186320803360.319299062231-0.29402188829-0.007586067729590.1269403836360.3189774091340.164751122928-0.11578611716-0.02232309356130.289501602351-0.08925134120560.03136407332950.222078057007-0.06631410115220.457248206253-13.8575535767-38.185092951734.3750129835
130.827575486257-0.07535498589870.1967639523513.004341867381.667781259571.55443729683-0.04204276154-0.156621119273-0.0929849955840.008956467632160.06385478116280.171264920412-0.09511635294180.086650080976-8.48916051938E-50.289344556234-0.0005451157920820.05942418098240.2264762732120.04665638939370.199807399034-3.20466136232-17.724268761257.1364865512
140.9813621002690.110084390673-0.04473130661180.9228645752590.4034394984011.4742930758-0.140856890856-0.0346516267952-0.2693281873540.1486630448370.03976334074820.1170418678170.1099961629920.06567383632820.1027323382710.25249521498-0.02203565879560.03890089072640.1273933385820.05445906453650.236873761946-1.34933607018-24.724092112646.9685561883
150.8262395070620.38623861504-0.03880720768711.26833072695-0.4456370981142.24209647754-0.1131536949710.429586257937-0.105371407279-0.181909863305-0.00151521052731-0.04963667663330.288704773746-0.2274251448890.09560512149810.206992662898-0.02017113255430.04866013743430.329832862619-0.05205025787790.17967793309310.0319204968-17.790701880317.4084504331
162.775848066090.380055076704-0.5634756813420.799372600828-0.3181189281810.9388213385890.106106534817-0.2747421071970.4596078024610.0591762834204-0.0517395125397-0.118230208057-0.1295620287970.242443608698-0.0602155861270.223236223868-0.04893234967010.01710141818550.245732402123-0.0554170285360.21873989413827.9464360655-2.4369363731432.6062437617
171.97217743957-0.3301576977520.2183474640261.7268236713-0.7835156034232.419933762820.1304178012610.608164600679-0.0874572764596-0.263087991107-0.0289115525510.09364293233850.0716537000446-0.164603446402-0.06994148878710.191927227310.006401986892080.03755043651540.36632284194-0.005023934096080.177220322259.84035011867-14.094499325715.0703686724
184.84807389392-0.7070012840150.2888413723911.28156652925-0.3822571061071.196470790760.1394370701790.261493950523-0.0199057629047-0.045496508664-0.0857490515123-0.08640626495750.0176019855870.106395068639-0.06995802949570.209060058555-0.002015466302560.02855238379720.2526157884570.02657101890490.13881289954829.8827592931-9.3213665983517.5049141891
192.89319167746-0.07467190147980.01000283988760.506001504874-0.1435016747141.014842396710.2344542276730.5167771309520.1506245335580.00570059178006-0.136109398975-0.00288794293211-0.0369532679939-0.269412141083-0.09158533944340.175333841845-0.00122189653842-0.007275161705880.2618355480090.03884025471360.18511230760917.0033661779-7.3167590830117.8394172932
203.271234278630.5826481486540.2094808381910.917020529449-0.05568562818793.064689755060.004487288674520.1482778601850.1156688733640.102379295222-0.017008963762-0.251061035911-0.01295260659430.4459478558770.05653379484580.208481503628-0.019506283644-0.04217417646450.162743091389-0.02536944579740.278985310305-32.0354943703-11.136160088232.0096841882
210.680871681076-0.319863887956-0.1540236744880.5429782599480.03907573806292.11039198899-0.0808271481005-0.1843469445640.01570369333250.1565135494880.0956116819990.05298051728570.100824719231-0.285681100884-0.01018607902610.2370659819110.00808060041091-0.001496643478010.205563517105-0.005739384722290.176481896737-54.6337017468-18.723917452945.7007904774
220.925527377569-0.01508155668680.2566156136591.927928757130.12712812761.42298064762-0.1806748983220.2141228434120.4722688696470.004946314247020.0885699394666-0.357785231876-0.4779604249370.3306479305640.08837779310130.333364193677-0.0756045981157-0.1035971592860.2361238898860.01418356867160.450501536154-30.31761124371.9269376362434.2391653717
230.8732301707960.536816683930.003543092880411.35549882057-0.7311204402041.26028504906-0.103096295696-0.0974644092203-0.02345981108050.0286084714370.00369934129285-0.01479745545780.102536964639-0.05276597122780.1094889263210.3868142827980.0299388272288-0.02089165720630.266993503974-0.04684990273380.167581397583-40.7277383788-21.269618807855.5113456833
241.68994074376-0.0996960056038-0.4547656903280.8859776371830.425007643451.63560724041-0.07511249709540.1444641125010.3704127522170.2059446638740.0562444887960.0494119476878-0.244779879135-0.0728301092171-0.02076385930870.299864265547-0.00482600598494-0.07044721714530.148707471861-0.01432262753970.299883260074-45.614805161-2.743781270833.558296307
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 65 )AA13 - 651 - 51
22chain 'A' and (resid 66 through 144 )AA66 - 14452 - 130
33chain 'A' and (resid 145 through 181 )AA145 - 181131 - 167
44chain 'A' and (resid 182 through 246 )AA182 - 246168 - 232
55chain 'A' and (resid 247 through 270 )AA247 - 270233 - 256
66chain 'A' and (resid 271 through 306 )AA271 - 306257 - 292
77chain 'A' and (resid 307 through 355 )AA307 - 355293 - 341
88chain 'A' and (resid 356 through 426 )AA356 - 426342 - 412
99chain 'A' and (resid 427 through 448 )AA427 - 448413 - 434
1010chain 'B' and (resid 13 through 106 )BC13 - 1061 - 93
1111chain 'B' and (resid 107 through 246 )BC107 - 24694 - 233
1212chain 'B' and (resid 247 through 270 )BC247 - 270234 - 257
1313chain 'B' and (resid 271 through 355 )BC271 - 355258 - 342
1414chain 'B' and (resid 356 through 448 )BC356 - 448343 - 435
1515chain 'C' and (resid 13 through 83 )CE13 - 831 - 68
1616chain 'C' and (resid 84 through 199 )CE84 - 19969 - 184
1717chain 'C' and (resid 200 through 270 )CE200 - 270185 - 255
1818chain 'C' and (resid 271 through 355 )CE271 - 355256 - 340
1919chain 'C' and (resid 356 through 450 )CE356 - 450341 - 435
2020chain 'D' and (resid 13 through 64 )DG13 - 641 - 51
2121chain 'D' and (resid 65 through 229 )DG65 - 22952 - 216
2222chain 'D' and (resid 230 through 284 )DG230 - 284217 - 271
2323chain 'D' and (resid 285 through 391 )DG285 - 391272 - 378
2424chain 'D' and (resid 392 through 449 )DG392 - 449379 - 436

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