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Yorodumi- PDB-3n98: Crystal structure of TK1436, a GH57 branching enzyme from hyperth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n98 | ||||||
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Title | Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives | ||||||
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: 1.87 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n98.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n98.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n98_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 3n98_full_validation.pdf.gz | 503.5 KB | Display | |
Data in XML | 3n98_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 3n98_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n98 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n98 | HTTPS FTP |
-Related structure data
Related structure data | 3n8tC 3n92C 1ufaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules A
#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 |
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#2: Sugar |
-Non-polymers , 5 types, 355 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % |
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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, 200 mM sodium chloride, 1% (v/v) dioxane and 5% (v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.87→68.08 Å / Num. obs: 59969 / % possible obs: 95.4 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5216 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UFA Resolution: 1.87→68.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.12 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→68.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.871→1.919 Å / Total num. of bins used: 20
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