[English] 日本語
Yorodumi- PDB-5fdf: Crystal structure of the monoclinic form of Thermotoga maritima A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fdf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the monoclinic form of Thermotoga maritima Acetyl Esterase TM0077 (apo structure) at 1.76 Angstrom resolution | ||||||
Components | Cephalosporin-C deacetylase | ||||||
Keywords | HYDROLASE / carbohydrate metabolism / cephalosporin deacetylase / Rossmann fold | ||||||
Function / homology | Function and homology information xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Manoj, N. / Singh, M.K. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability. Authors: Singh, M.K. / Manoj, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fdf.cif.gz | 413.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fdf.ent.gz | 332.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fdf ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fdf | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hfnC 1vlqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38662.922 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: cytoplasm / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: axeA, TM_0077 / Plasmid: pMH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: Q9WXT2, cephalosporin-C deacetylase, acetylxylan esterase #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5 and 30% (V/V) Pentaerythritol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.76→39.96 Å / Num. obs: 194397 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.047 / Net I/σ(I): 11.5 / Num. measured all: 1297873 / Scaling rejects: 291 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VLQ Resolution: 1.76→39.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.576 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / SU Rfree Cruickshank DPI: 0.1058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.28 Å2 / Biso mean: 21.9 Å2 / Biso min: 10.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→39.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Highest resolution: 1.76 Å |