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Yorodumi- PDB-5ddw: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ddw | |||||||||
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Title | Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with the PMP external aldimine adduct with Caerulomycin M | |||||||||
Components | CrmG | |||||||||
Keywords | TRANSFERASE / Aminotransferase / Caerulomycin M / Caerulomycin Biosynthesis | |||||||||
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: 2.3 Å | |||||||||
Authors | Xu, J. / Feng, Z. / Liu, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis Authors: Zhu, Y. / Xu, J. / Mei, X. / Feng, Z. / Zhang, L. / Zhang, Q. / Zhang, G. / Zhu, W. / Liu, J. / Zhang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ddw.cif.gz | 402.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ddw.ent.gz | 329.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ddw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ddw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ddw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5ddw_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 5ddw_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/5ddw ftp://data.pdbj.org/pub/pdb/validation_reports/dd/5ddw | HTTPS FTP |
-Related 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: _ / Refine code: _
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-5B6 / [ #3: Chemical | ChemComp-GOL / #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: 2.39 Å3/Da / Density % sol: 48.6 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG3350, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→49.25 Å / Num. obs: 86965 / % possible obs: 92.2 % / Redundancy: 4.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.074 / Net I/σ(I): 8.1 / Num. measured all: 398069 / Scaling rejects: 202 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2325 / WRfactor Rwork: 0.1928 / FOM work R set: 0.8209 / SU B: 7.933 / SU ML: 0.188 / SU R Cruickshank DPI: 0.4656 / SU Rfree: 0.2561 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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: 136.8 Å2 / Biso mean: 27.183 Å2 / Biso min: 3.35 Å2
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Refinement step | Cycle: final / Resolution: 2.3→49.25 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: 2.3→2.36 Å / Total num. of bins used: 20
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