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- PDB-1huv: CRYSTAL STRUCTURE OF A SOLUBLE MUTANT OF THE MEMBRANE-ASSOCIATED ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1huv | ||||||
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Title | CRYSTAL STRUCTURE OF A SOLUBLE MUTANT OF THE MEMBRANE-ASSOCIATED (S)-MANDELATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA AT 2.15A RESOLUTION | ||||||
![]() | L(+)-MANDELATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / TIM BARREL | ||||||
Function / homology | ![]() (S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase (NAD+) activity / aerobic respiration / peroxisome ...(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase (NAD+) activity / aerobic respiration / peroxisome / FMN binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mathews, F.S. / Sukumar, N. | ||||||
![]() | ![]() Title: Structure of an active soluble mutant of the membrane-associated (S)-mandelate dehydrogenase. Authors: Sukumar, N. / Xu, Y. / Gatti, D.L. / Mitra, B. / Mathews, F.S. | ||||||
History |
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Remark 999 | Sequence chimeric mutant of (s)-mandelate dehydrogenase with residues 177-215 replaced by residues ...Sequence chimeric mutant of (s)-mandelate dehydrogenase with residues 177-215 replaced by residues 176-195 of glycolate oxidase. The authors believe SwissProt entry P20932 incorrectly lists residue 15 as ARG instead of ALA. Sequencing of MDH, as well as the original clone pSCR4, has been done a number of times including site-specific mutants and repeatedly confirmed that it is ALA 15 rather than ARG 15. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.2 KB | Display | ![]() |
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Full document | ![]() | 795.6 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1goxS 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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1 | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by crystallographic 4-fold axes. |
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Components
#1: Protein | Mass: 42132.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 20 RESIDUE INSERTION FROM GLYCOLATE OXIDASE AT RESIDUE 177 Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: MES, ammonium sulfate, ethylene glycerol, FMN, NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 28882 / Num. obs: 28143 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.7 Å2 / Rsym value: 9.2 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.15→30 Å / Mean I/σ(I) obs: 6.3 / Rsym value: 36.2 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.362 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() ![]() Starting model: PDB ENTRY 1GOX Resolution: 2.15→27.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 53281.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.08 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→27.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.175 |