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- PDB-2yq5: Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yq5 | ||||||
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Title | Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus: NAD complexed form | ||||||
![]() | D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE | ||||||
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Function / homology | ![]() oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M. | ||||||
![]() | ![]() Title: Structural Characterization of D-Isomer Specific 2-Hydroxyacid Dehydrogenase from Lactobacillus Delbrueckii Ssp. Bulgaricus Authors: Holton, S.J. / Anandhakrishnan, M. / Geerlof, A. / Wilmanns, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 509.5 KB | Display | ![]() |
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PDB format | ![]() | 425.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yq4C ![]() 1dxyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 38029.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PETM-13 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow![]() | Details: 25% PEG 3350, 200MM MGCL2, 100MM HEPES PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.75→49.24 Å / Num. obs: 39722 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1DXY Resolution: 2.75→44.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 28.999 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
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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: 47.897 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→44.99 Å
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Refine LS restraints |
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