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- PDB-7c49: nicA2 with cofactor FAD and substrate nicotine -

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Basic information

Entry
Database: PDB / ID: 7c49
TitlenicA2 with cofactor FAD and substrate nicotine
ComponentsAmine oxidase
KeywordsOXIDOREDUCTASE / complex / oxydoreductase
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 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / Nicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida S16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.25 Å
AuthorsXu, P. / Zhang, K.
CitationJournal: Mbio / Year: 2020
Title: Molecular Deceleration Regulates Toxicant Release to Prevent Cell Damage in Pseudomonas putida S16 (DSM 28022).
Authors: Tang, H. / Zhang, K. / Hu, H. / Wu, G. / Wang, W. / Zhu, X. / Liu, G. / Xu, P.
History
DepositionMay 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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)104,8476
Polymers102,9202
Non-polymers1,9284
Water3,639202
1
A: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4243
Polymers51,4601
Non-polymers9642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4243
Polymers51,4601
Non-polymers9642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.787, 81.787, 164.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -0.000158, 0.000133), (-0.000158, 1, 0.000274), (-0.000133, 0.000274, -1)0.00623, 0.00457, -1.4625

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Components

#1: Protein Amine oxidase


Mass: 51459.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida S16 (bacteria) / Strain: S16 / Gene: PPS_4081 / Production host: Escherichia coli (E. coli) / References: UniProt: F8G0P2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-HNL / 5-[(2S)-1-methylpyrrolidin-2-yl]pyridin-2-ol / 6-hydroxy-L-nicotine


Mass: 178.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Tris-Hcl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→81.79 Å / Num. obs: 51361 / % possible obs: 95.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.6
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.529 / Num. unique obs: 5128

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.25→39.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.303 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 2621 5.3 %RANDOM
Rwork0.176 ---
obs0.178 46537 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 109.72 Å2 / Biso mean: 52.906 Å2 / Biso min: 22.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å20 Å2
2--2.98 Å20 Å2
3----5.97 Å2
Refinement stepCycle: final / Resolution: 2.25→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 130 202 6988
Biso mean--51.74 44.81 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0187048
X-RAY DIFFRACTIONr_bond_other_d0.0010.026430
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.8719556
X-RAY DIFFRACTIONr_angle_other_deg1.0532.91714860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44223.834326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291547
X-RAY DIFFRACTIONr_chiral_restr0.0790.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021488
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.306 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.236 188 -
Rwork0.18 3588 -
obs--99.06 %
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)
10.5516-0.1072-0.06961.9779-0.11311.0414-0.0456-0.0315-0.15550.16510.05190.03590.2663-0.0484-0.00630.104-0.010.0020.02330.00050.0833-6.034-22.61515.977
20.2004-0.0437-0.10661.90740.12440.9539-0.04580.0231-0.0967-0.12810.0556-0.05620.27260.0788-0.00980.11190.01570.00930.0455-0.00630.11655.832-23.059-17.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 482
2X-RAY DIFFRACTION2B50 - 483

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