+Open data
-Basic information
Entry | Database: PDB / ID: 7zbo | ||||||
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Title | Amine Dehydrogenase MATOUAmDH2 in complex with NADP+ | ||||||
Components | Amine Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Amine / NADP+ / dehydrogenase | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Bennett, M. / Ducrot, L. / Vergne-Vaxelaire, C. / Grogan, G. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2022 Title: Structure and Mutation of the Native Amine Dehydrogenase MATOUAmDH2. Authors: Bennett, M. / Ducrot, L. / Vergne-Vaxelaire, C. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zbo.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zbo.ent.gz | 217.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/7zbo ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zbo | HTTPS FTP |
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-Related structure data
Related structure data | 7r09C 6iauS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 38249.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 1.4.9.98 #2: Chemical | ChemComp-NAP / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate; 0.1 M bis-tris propane; 25% (w/v) PEG3350; 10% (v/v) methylpentanediol |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→64.21 Å / Num. obs: 68673 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.14 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.32→2.37 Å / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4580 / CC1/2: 0.68 / Rpim(I) all: 0.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IAU Resolution: 2.32→64.21 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.371 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.59 Å2 / Biso mean: 35.175 Å2 / Biso min: 11.3 Å2
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Refinement step | Cycle: final / Resolution: 2.32→64.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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