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Yorodumi- PDB-6jc8: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jc8 | ||||||
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Title | Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Glu | ||||||
Components | CrmG | ||||||
Keywords | TRANSFERASE / aminotransferase / CrmG / Amino donor | ||||||
Function / homology | Function and homology information transaminase activity / pyridoxal phosphate binding / identical protein binding Similarity search - Function | ||||||
Biological species | Actinoalloteichus sp. WH1-2216-6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Xu, J. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2020 Title: Structural studies reveal flexible roof of active site responsible for omega-transaminase CrmG overcoming by-product inhibition. Authors: Xu, J. / Tang, X. / Zhu, Y. / Yu, Z. / Su, K. / Zhang, Y. / Dong, Y. / Zhu, W. / Zhang, C. / Wu, R. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jc8.cif.gz | 404.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jc8.ent.gz | 329.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/6jc8 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/6jc8 | HTTPS FTP |
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-Related structure data
Related structure data | 6jc7C 6jc9C 6jcaC 6jcbC 5ddsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 6 - 522 / Label seq-ID: 6 - 522
NCS ensembles :
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-Components
#1: Protein | Mass: 57219.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinoalloteichus sp. WH1-2216-6 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H8Y6N2 #2: Chemical | ChemComp-PL6 / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.15 % / Mosaicity: 0.48 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG 3350, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→49.46 Å / Num. obs: 96761 / % possible obs: 95 % / Redundancy: 3.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Net I/σ(I): 8.6 / Num. measured all: 380457 / Scaling rejects: 145 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DDS Resolution: 2.25→49.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2049 / WRfactor Rwork: 0.1682 / FOM work R set: 0.8386 / SU B: 6.451 / SU ML: 0.153 / SU R Cruickshank DPI: 0.3274 / SU Rfree: 0.2114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. 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: 117.05 Å2 / Biso mean: 29.293 Å2 / Biso min: 10.22 Å2
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Refinement step | Cycle: final / Resolution: 2.25→49.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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