+Open data
-Basic information
Entry | Database: PDB / ID: 7c4a | ||||||
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Title | nicA2 with cofactor FAD | ||||||
Components | Amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Pseudomonas putida S16 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.05 Å | ||||||
Authors | Xu, P. / Zang, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c4a.cif.gz | 353.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c4a.ent.gz | 297.7 KB | Display | PDB format |
PDBx/mmJSON format | 7c4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/7c4a ftp://data.pdbj.org/pub/pdb/validation_reports/c4/7c4a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: pet3350, tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2016 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.77 Å2 / Biso mean: 27.387 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: final / Resolution: 2.05→37.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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