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Yorodumi- PDB-6abj: The apo-structure of D-lactate dehydrogenase from Pseudomonas aer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6abj | |||||||||
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Title | The apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa | |||||||||
Components | D-lactate dehydrogenase (Fermentative) | |||||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H. | |||||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria Authors: Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6abj.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6abj.ent.gz | 212.3 KB | Display | PDB format |
PDBx/mmJSON format | 6abj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6abj_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 6abj_full_validation.pdf.gz | 459 KB | Display | |
Data in XML | 6abj_validation.xml.gz | 26 KB | Display | |
Data in CIF | 6abj_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/6abj ftp://data.pdbj.org/pub/pdb/validation_reports/ab/6abj | HTTPS FTP |
-Related structure data
Related structure data | 5z1zC 5z20C 5z21C 6abiC 1j49S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 326 / Label seq-ID: 17 - 342
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-Components
#1: Protein | Mass: 37832.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ldhA, PA0927 / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q9I530 #2: Chemical | #3: 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: 54.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium acetate (pH 5.5), 8% PEG3350, and 50 mM magnesium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→52.26 Å / Num. obs: 68606 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.04 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9844 / CC1/2: 0.774 / Rpim(I) all: 0.349 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J49 Resolution: 1.86→52.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.426 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / 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: 37.809 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→52.26 Å
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Refine LS restraints |
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