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Yorodumi- PDB-8ahr: Crystal structure of D-amino acid aminotransferase from Aminobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ahr | ||||||
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Title | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense in holo form with PLP | ||||||
Components | Aminotransferase class IV | ||||||
Keywords | TRANSFERASE / Transaminase / DAAT / aminotransferase | ||||||
Function / homology | Function and homology information carboxylic acid biosynthetic process / organonitrogen compound biosynthetic process / transaminase activity Similarity search - Function | ||||||
Biological species | Aminobacterium colombiense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Matyuta, I.O. / Boyko, K.M. / Nikolaeva, A.Y. / Shilova, S.A. / Rakitina, T.V. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Molecules / Year: 2023 Title: To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense. Authors: Shilova, S.A. / Khrenova, M.G. / Matyuta, I.O. / Nikolaeva, A.Y. / Rakitina, T.V. / Klyachko, N.L. / Minyaev, M.E. / Boyko, K.M. / Popov, V.O. / Bezsudnova, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ahr.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ahr.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ahr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ahr ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ahr | HTTPS FTP |
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-Related structure data
Related structure data | 8aykC 5mqzS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: -1 - 275 / Label seq-ID: 1 - 277
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-Components
#1: Protein | Mass: 30976.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aminobacterium colombiense (bacteria) / Strain: DSM 12261 / ALA-1 / Gene: Amico_1844 / Production host: Escherichia coli (E. coli) / References: UniProt: D5EHC5 #2: Chemical | #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: 1.98 Å3/Da / Density % sol: 37.83 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium nitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→43.78 Å / Num. obs: 38455 / % possible obs: 98.1 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.047 / Rrim(I) all: 0.094 / Net I/σ(I): 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MQZ Resolution: 1.9→43.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2361 / WRfactor Rwork: 0.1799 / FOM work R set: 0.7506 / SU B: 5.491 / SU ML: 0.15 / SU R Cruickshank DPI: 0.1898 / SU Rfree: 0.1725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172 / 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: 109.99 Å2 / Biso mean: 32.811 Å2 / Biso min: 19.76 Å2
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Refinement step | Cycle: final / Resolution: 1.9→43.78 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8170 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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