[English] 日本語
Yorodumi- PDB-3n8t: Native structure of TK1436, a GH57 branching enzyme from hyperthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n8t | ||||||
---|---|---|---|---|---|---|---|
Title | Native structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis | ||||||
Components | alpha-amylase, GH57 family | ||||||
Keywords | TRANSFERASE / GH57 family member / branching enzyme | ||||||
Function / homology | Function and homology information alpha-glucan biosynthetic process / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Santos, C.R. / Tonoli, C.C.C. / Trindade, D.M. / Betzel, C. / Takata, H. / Kuriki, T. / Kanai, T. / Imanaka, T. / Arni, R.K. / Murakami, M.T. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structural basis for branching-enzyme activity of glycoside hydrolase family 57: Structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus Kodakaraensis KOD1. Authors: Santos, C.R. / Tonoli, C.C. / Trindade, D.M. / Betzel, C. / Takata, H. / Kuriki, T. / Kanai, T. / Imanaka, T. / Arni, R.K. / Murakami, M.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n8t.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n8t.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n8t_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3n8t_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 3n8t_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3n8t_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/3n8t ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n8t | HTTPS FTP |
-Related structure data
Related structure data | 3n92C 3n98C 1ufaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66167.953 Da / Num. of mol.: 1 / Fragment: UNP residues 1-562 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1436 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q5JDJ7, 1,4-alpha-glucan branching enzyme |
---|---|
#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-PG4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM sodium acetate (pH 5.5), 15% (w/v) PEG 8000, 10% (v/v) PEG 400 and 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Monochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→68.1 Å / Num. obs: 29790 / % possible obs: 99.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2906 / % possible all: 98.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UFA Resolution: 2.4→68.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.93 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.958 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→68.05 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|