[English] 日本語
Yorodumi- PDB-7xg9: Crystal structural of methylenetetrahydrofolate reductase from Sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xg9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6 | ||||||
Components | 5,10-methylenetetrahydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / CH3-THF oxidation / Non-NADH/NAD+ binding type / TIM barrel / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine metabolic process / tetrahydrofolate interconversion Similarity search - Function | ||||||
Biological species | Sphingobium sp. SYK-6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Yu, H.Y. / Senda, M. / Senda, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6 Authors: Yu, H.Y. / Senda, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xg9.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xg9.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xg9 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xg9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7xlfC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31362.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Strain: NBRC 103272 / SYK-6 / Gene: metF, SLG_12750 / Plasmid: pET44a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: G2IQS8, methylenetetrahydrofolate reductase [NAD(P)H] #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.32 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 4.5 / Temp details: 4 degC |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→42.35 Å / Num. obs: 84735 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.031 / Rrim(I) all: 0.046 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4091 / CC1/2: 0.913 / Rpim(I) all: 0.215 / Rrim(I) all: 0.322 / % possible all: 96.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.5→34.92 Å / SU ML: 0.1427 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6977 / Stereochemistry target values: CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|