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Yorodumi- PDB-6rts: Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rts | ||||||
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Title | Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with NAD+ | ||||||
Components | Semialdehyde dehydrogenase Pcd | ||||||
Keywords | OXIDOREDUCTASE / antibiotic biosynthesis / Streptomyces clavuligerus | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity Similarity search - Function | ||||||
Biological species | Streptomyces clavuligerus ATCC 27064 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Hasse, D. / Huelsemann, J. / Carlsson, G. / Andersson, I. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus. Authors: Hasse, D. / Hulsemann, J. / Carlsson, G.H. / Valegard, K. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rts.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rts.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/6rts ftp://data.pdbj.org/pub/pdb/validation_reports/rt/6rts | HTTPS FTP |
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-Related structure data
Related structure data | 6rtrSC 6rttC 6rtuC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54088.996 Da / Num. of mol.: 2 / Mutation: S140T A503T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus ATCC 27064 (bacteria) Gene: pcd / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: O85725 |
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-Non-polymers , 5 types, 561 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0,1 M sodium acetate pH 5, 2.2 M ammonium sulphate, 0.2 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.4 Å / Num. obs: 54522 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.8 Å2 / Rrim(I) all: 0.159 / Net I/σ(I): 8.32 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.22 / Num. unique obs: 5800 / Rrim(I) all: 0.663 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RTR Resolution: 2.25→45.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.961 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→45.4 Å
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Refine LS restraints |
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