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- PDB-7c4a: nicA2 with cofactor FAD -

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Basic information

Entry
Database: PDB / ID: 7c4a
TitlenicA2 with cofactor FAD
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 / Nicotine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida S16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.05 Å
AuthorsXu, P. / Zang, 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)98,5264
Polymers96,9542
Non-polymers1,5712
Water9,458525
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.693, 115.693, 168.531
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.116647, 0.993168, -0.00321), (0.993171, 0.116638, -0.002756), (-0.002363, -0.003509, -0.999991)64.570686, -57.494068, 0.32128

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Components

#1: Protein Amine oxidase


Mass: 48477.242 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: pet3350, tris

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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 315r / Detector: CCD / Date: May 4, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→95.38 Å / Num. obs: 72574 / % possible obs: 99.79 % / Redundancy: 8.1 % / CC1/2: 0.99 / CC star: 0.99 / Rpim(I) all: 0.054 / Rrim(I) all: 0.154 / Net I/σ(I): 102.2
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 7139 / CC1/2: 0.9 / CC star: 0.97 / Rpim(I) all: 0.229 / Rrim(I) all: 0.662

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.05→37.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.71 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.123 / 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
Rfree0.19 3641 5 %RANDOM
Rwork0.1511 ---
obs0.1526 68576 99.51 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 101.77 Å2 / Biso mean: 27.387 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2--0.79 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 2.05→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 106 525 7390
Biso mean--16.2 32.12 -
Num. residues----871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0187019
X-RAY DIFFRACTIONr_bond_other_d0.0010.026421
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.8719528
X-RAY DIFFRACTIONr_angle_other_deg1.1262.88514838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49323.851322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.511151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5771548
X-RAY DIFFRACTIONr_chiral_restr0.0950.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
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: 2.05→2.1 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.218 253 -
Rwork0.197 5036 -
obs--99.74 %
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)
10.66210.3921-0.16570.8697-0.13240.64620.0181-0.0248-0.02770.091-0.0130.08070.0519-0.1136-0.00510.0297-0.01210.00920.03830.0040.01838.027-12.78717.213
21.17210.746-0.32011.1297-0.26121.0031-0.16410.2249-0.1021-0.16110.15030.00720.2624-0.13310.01380.0919-0.04750.00610.0605-0.01830.022847.522-21.21-16.887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 485
2X-RAY DIFFRACTION2B50 - 485

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