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Yorodumi- PDB-6rxh: In-flow serial synchrotron crystallography using a 3D-printed mic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rxh | |||||||||
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Title | In-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Aspartate alpha-decarboxylase | |||||||||
Components | (Aspartate 1-decarboxylase) x 2 | |||||||||
Keywords | LYASE | |||||||||
Function / homology | Function and homology information alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Monteiro, D.C.F. / von Stetten, D. / Pearson, A.R. / Trebbin, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Iucrj / Year: 2020 Title: 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow. Authors: Monteiro, D.C.F. / von Stetten, D. / Stohrer, C. / Sans, M. / Pearson, A.R. / Santoni, G. / van der Linden, P. / Trebbin, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxh.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxh.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 6rxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rxh_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 6rxh_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 6rxh_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6rxh_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxh ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxh | HTTPS FTP |
-Related structure data
Related structure data | 6rxiC 1aw8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1631290 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4770.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ADC beta-chain after post-translational modification Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panD, DNX30_02475 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A403CTL2, UniProt: P0A790*PLUS, aspartate 1-decarboxylase #2: Protein | Mass: 11010.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ADC alpha-chain after post-translational modification Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panD, DN623_10270 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A3U0WEI2, UniProt: P0A790*PLUS, aspartate 1-decarboxylase #3: Chemical | ChemComp-UNX / #4: 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: 2.6 Å3/Da / Density % sol: 52.78 % / Description: cuboid microcrystals |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 3.8 Details: 1:3 protein:mother liquor mixture. 25 mg/mL of ADC in 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1 mM DTT. Mother liquor: 1.95 M (NH4)2SO4, 100 mM citrate/di-sodium phosphate buffer pH 3.8 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2→63.05 Å / Num. obs: 24287 / % possible obs: 100 % / Redundancy: 6006 % / Biso Wilson estimate: 30.5 Å2 / R split: 0.04 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 4356 % / Num. unique obs: 2374 / R split: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AW8 Resolution: 2→63.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.699 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.161 Å2
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Refinement step | Cycle: LAST / Resolution: 2→63.05 Å
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Refine LS restraints |
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