[English] 日本語
Yorodumi- PDB-1p4c: High Resolution Structure of Oxidized Active Mutant of (S)-Mandel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4c | ||||||
---|---|---|---|---|---|---|---|
Title | High Resolution Structure of Oxidized Active Mutant of (S)-Mandelate Dehydrogenase | ||||||
Components | L(+)-Mandelate Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / TIM BARREL / Hydroxy acid oxidizing enzyme | ||||||
Function / homology | Function and homology information (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 / : / fatty acid alpha-oxidation / response to other organism / L-lactate dehydrogenase activity ...(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 / : / fatty acid alpha-oxidation / response to other organism / L-lactate dehydrogenase activity / peroxisome / FMN binding / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Sukumar, N. / Mitra, B. / Mathews, F.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: High Resolution Structures of an Oxidized and Reduced Flavoprotein: THE WATER SWITCH IN A SOLUBLE FORM OF (S)-MANDELATE DEHYDROGENASE Authors: Sukumar, N. / Dewanti, A.R. / Mitra, B. / Mathews, F.S. #1: Journal: Biochemistry / Year: 2001 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 |
| ||||||
Remark 999 | SEQUENCE Chimeric mutant of (s)-mandelate dehydrogenase with residues 177-196 replaced by residues ...SEQUENCE Chimeric mutant of (s)-mandelate dehydrogenase with residues 177-196 replaced by residues 176- 195 of glycolate oxidase. The authors believe that SwissProt entry P20932 incorrectly lists residue 15 as ARG instead of ALA. Sequencing of (s)-mandelate dehydrogenase, as well as of the original clone pSCR4, has been done a number of times including site-specific mutants and has repeatedly confirmed that it is ALA 15 rather than ARG 15. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1p4c.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1p4c.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p4c_validation.pdf.gz | 799 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1p4c_full_validation.pdf.gz | 808.8 KB | Display | |
Data in XML | 1p4c_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1p4c_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4c ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4c | HTTPS FTP |
-Related structure data
Related structure data | 1p5bC 1huvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42132.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 20 RESIDUE SUBSTITUTION FROM GLYCOLATE OXIDASE AT RESIDUE 177 Source: (gene. exp.) Pseudomonas putida (bacteria), (gene. exp.) Spinacia oleracea (spinach) Production host: Escherichia coli (E. coli) / References: UniProt: P20932, UniProt: P05414 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.82 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: ammonium sulfate, ethylene glycol, FMN, Sodium Chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sukumar, N., (2001) Biochemistry, 40, 9870. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97625 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 92753 / % possible obs: 99.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.279 / % possible all: 98.1 |
Reflection | *PLUS Lowest resolution: 500 Å / Num. obs: 91731 / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.282 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HUV Resolution: 1.35→39.6 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 240668.51 / Data cutoff high rms absF: 240668.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3837 Å2 / ksol: 0.352965 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→39.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.4 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|