[English] 日本語
Yorodumi- PDB-2ecr: Crystal structure of the ligand-free form of the flavin reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ecr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ligand-free form of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase | ||||||
Components | flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Flavin reductase / flavin diffusible / two-component monooxygenase | ||||||
Function / homology | Function and homology information flavin reductase (NADH) / flavin reductase (NADH) activity / pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / : / FMN binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kim, S.H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity Authors: Kim, S.H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallization and preliminary X-ray analysis of the small component of 4-hydroxyphenylacetate 3-monooxygenase (HpaC) and its cofactor complex from Thermus thermophilus HB8 Authors: Kim, S.H. / Miyatake, H. / Hisano, T. / Ohtani, N. / Miki, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ecr.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ecr.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2ecr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ecr_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ecr_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 2ecr_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2ecr_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2ecr ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2ecr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16059.578 Da / Num. of mol.: 2 / Mutation: E131G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0961 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJP7, EC: 1.6.8.- #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40% PEG 4000, 5% isopropyl alcohol, 0.1M HEPES-NaOH, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 27, 2002 / Details: mirrors |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 35392 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 13.466 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3505 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Selenomethionine-labeled crystal was used for phase determination, and the model was used for initial target model. Resolution: 1.6→41.4 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→41.4 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|