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- PDB-5ttj: Crystal Structure of Nicotine Oxidoreductase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 5ttj
TitleCrystal Structure of Nicotine Oxidoreductase from Pseudomonas putida
ComponentsAmine oxidase
KeywordsOXIDOREDUCTASE / nicotine degradation / flavoenzyme / monoamine oxidase family / PHBH fold
Function / homology
Function and homology information


nicotine dehydrogenase / nicotine catabolic process / alkaloid metabolic process / periplasmic space / oxidoreductase activity / nucleotide binding
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Nicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTararina, M.A. / Janda, K.D. / Allen, K.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA041839 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008541 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida.
Authors: Tararina, M.A. / Janda, K.D. / Allen, K.N.
History
DepositionNov 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 11, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9024
Polymers107,3312
Non-polymers1,5712
Water4,486249
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4512
Polymers53,6651
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4512
Polymers53,6651
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.973, 61.564, 92.277
Angle α, β, γ (deg.)90.00, 92.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amine oxidase /


Mass: 53665.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain S16) (bacteria)
Strain: S16 / Gene: PPS_4081
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F8G0P2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 31.56 %
Description: long, rectangular, yellow plate-shaped crystals of approximately 0.1 mm by 0.2 mm by 0.8 mm dimensions
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4% v/v 2-propanol, 0.1 M BIS-TRIS propane pH 9.0 and 20% w/v polyethylene glycol (PEG)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→92.27 Å / Num. obs: 38640 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 5.6 / CC1/2: 0.91 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155model building
RefinementResolution: 2.2→92.188 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1095 2.94 %
Rwork0.1748 --
obs0.1764 37193 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→92.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6743 0 106 249 7098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077001
X-RAY DIFFRACTIONf_angle_d0.9819503
X-RAY DIFFRACTIONf_dihedral_angle_d16.4464041
X-RAY DIFFRACTIONf_chiral_restr0.0571037
X-RAY DIFFRACTIONf_plane_restr0.0061217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30020.30661270.22554410X-RAY DIFFRACTION94
2.3002-2.42140.32141280.21594477X-RAY DIFFRACTION95
2.4214-2.57320.29781470.20694447X-RAY DIFFRACTION95
2.5732-2.77180.29291300.20184586X-RAY DIFFRACTION97
2.7718-3.05080.26071410.19844542X-RAY DIFFRACTION97
3.0508-3.49230.23011430.17124514X-RAY DIFFRACTION96
3.4923-4.39990.1711360.14234502X-RAY DIFFRACTION94
4.3999-92.26920.19531430.15354620X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.6364-0.20440.29240.396-0.34740.7922-0.00040.0367-0.05550.0149-0.0779-0.05940.1150.00750.05810.23-0.0118-0.02040.0727-0.01260.1993-36.2654-7.4145-20.2499
22.360.55140.64742.07581.14070.74470.00540.26330.1985-0.26680.0377-0.2118-0.20550.3153-0.0410.3263-0.00650.11760.58170.14760.3708-22.83771.6537-45.9997
30.5780.0040.19840.7406-0.32670.90760.06110.2898-0.0027-0.0946-0.0743-0.11910.44590.47180.05830.36890.096-0.00260.27940.06470.3015-24.0785-13.6643-23.1518
40.8062-0.0250.27370.64-0.09681.0293-0.05690.21440.145-0.0477-0.27-0.1960.12950.45720.06490.23390.0298-0.00340.08270.0620.2486-29.7175-1.7909-27.8169
50.5680.04560.0690.3449-0.3690.4122-0.02540.16050.00020.03130.02140.0448-0.1242-0.5697-0.04170.17560.0592-0.01280.3995-0.02110.21268.17738.0075-38.565
61.52950.0731-0.55880.3922-0.25140.33070.1064-0.11620.18340.24260.0350.0851-0.2011-0.2198-0.12560.27180.04950.00480.2432-0.02180.234617.4710.291-23.0251
70.9034-0.55060.01372.46150.47040.9326-0.0784-0.16270.06770.4657-0.09980.1036-0.224-0.42080.09020.552-0.01030.12680.556-0.00850.30170.87216.7675-2.227
81.0348-0.1771-0.67440.3375-0.01610.9787-0.1046-0.0477-0.11420.3185-0.03890.2210.3069-0.43070.08710.3528-0.17520.10940.483-0.0140.32333.4377-12.8899-14.7037
91.2371-0.25320.48311.51380.13910.22670.0421-0.05610.03090.4024-0.10550.38420.0389-0.59210.09040.3216-0.10350.14760.6764-0.06540.3655-1.1188-1.3632-12.9889
100.38520.05180.17040.461-0.17620.481-0.07940.06150.00940.05490.03120.1385-0.0846-0.68770.1390.19170.0275-0.02670.4332-0.00780.22517.8835.6762-35.286
110.28630.089-0.07120.5724-0.24170.7855-0.05750.3141-0.05990.20070.15650.3009-0.1374-0.39350.16870.04930.0370.03910.8166-0.06540.3383-3.32886.7695-27.9445
120.94750.5946-0.36952.97780.31181.0468-0.1710.16960.27690.02270.02260.4379-0.3511-0.3112-0.00880.44920.10160.10220.6959-0.01540.415-7.49619.7644-15.6779
130.33030.235-0.20440.4258-0.16560.7412-0.0160.0595-0.06110.1330.01490.12890.112-0.73560.01910.16-0.0430.00260.5603-0.02630.22552.060.4691-31.2037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 269 )
2X-RAY DIFFRACTION2chain 'A' and (resid 270 through 292 )
3X-RAY DIFFRACTION3chain 'A' and (resid 293 through 403 )
4X-RAY DIFFRACTION4chain 'A' and (resid 404 through 483 )
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 166 )
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 204 )
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 237 )
10X-RAY DIFFRACTION10chain 'B' and (resid 238 through 293 )
11X-RAY DIFFRACTION11chain 'B' and (resid 294 through 371 )
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 403 )
13X-RAY DIFFRACTION13chain 'B' and (resid 404 through 482 )

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