[English] 日本語
Yorodumi- PDB-8crd: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8crd | ||||||
---|---|---|---|---|---|---|---|
Title | Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position | ||||||
Components | Ferulic acid decarboxylase 1 | ||||||
Keywords | LYASE / Decarboxylase / prFMN | ||||||
Function / homology | Function and homology information styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / manganese ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aspergillus niger CBS 513.88 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Roberts, G.W. / Leys, D. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position Authors: Roberts, G.W. / Leys, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8crd.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8crd.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 8crd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8crd ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8crd | HTTPS FTP |
---|
-Related structure data
Related structure data | 8oedC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56354.047 Da / Num. of mol.: 1 / Mutation: T40C S315C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger CBS 513.88 (mold) / Gene: fdc1, An03g06590 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QHE5, phenacrylate decarboxylase |
---|
-Non-polymers , 5 types, 560 molecules
#2: Chemical | ChemComp-BYN / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Chemical | ChemComp-SCN / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BIS-TRIS propane, potassium thiocyanate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 11, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→53.29 Å / Num. obs: 110958 / % possible obs: 93.5 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 10.6 % / Num. unique obs: 3493 / CC1/2: 0.3 / % possible all: 59.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→53.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.958 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.14 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.35→53.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|