[English] 日本語
Yorodumi- PDB-1g9h: TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA-AMYLASE, COMII (PSEUD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g9h | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | TERNARY COMPLEX BETWEEN PSYCHROPHILIC ALPHA-AMYLASE, COMII (PSEUDO TRI-SACCHARIDE FROM BAYER) AND TRIS (2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL) | |||||||||
Components | ALPHA-AMYLASE | |||||||||
Keywords | HYDROLASE / ALPHA-BETA 8 BARREL / 3 DOMAIN STRUCTURE | |||||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | |||||||||
Authors | Aghajari, N. / Roth, M. / Haser, R. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase. Authors: AGHAJARI, N. / ROTH, M. / HASER, R. #1: Journal: Structure / Year: 1998 Title: STRUCTURES OF THE PSYCHROPHILIC ALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE GIVE INSIGHTS INTO COLD ADAPTATION AT A MOLECULAR LEVEL Authors: AGHAJARI, N. / FELLER, G. / Gerday, C.H. / HASER, R. #2: Journal: Protein Sci. / Year: 1998 Title: CRYSTAL STRUCTURES OF THE PSYCHROPHILIC ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS IN ITS NATIVE FORM AND COMPLEXED WITH AN INHIBITOR Authors: AGHAJARI, N. / FELLER, G. / Gerday, C.H. / HASER, R. #3: Journal: Protein Sci. / Year: 1996 Title: CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF ALPHA-AMYLASE FROM THE ANTARCTIC PSYCHROPHILE ALTEROMONAS HALOPLANCTIS A23 Authors: AGHAJARI, N. / FELLER, G. / Gerday, C.H. / HASER, R. | |||||||||
History |
| |||||||||
Remark 600 | HETEROGEN HET GROUP USED IN THE FILE AS DAF IS ALSO KNOWN AS: ACARVIOSINE (VALIENAMINE + 4-AMINO-4, ...HETEROGEN HET GROUP USED IN THE FILE AS DAF IS ALSO KNOWN AS: ACARVIOSINE (VALIENAMINE + 4-AMINO-4, 6-DIDEOXY-A-D-GLUCOSE) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g9h.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g9h.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 1g9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g9h ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g9h | HTTPS FTP |
---|
-Related structure data
Related structure data | 1g94C 1kxhC 1aqhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 48947.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH TRI-SACCHARIDE AND TRIS / Source: (natural) Pseudoalteromonas haloplanktis (bacteria) / Strain: A23 / References: UniProt: P29957, alpha-amylase |
---|---|
#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5- ...4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose Type: oligosaccharide / Mass: 477.417 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 277 molecules
#3: Chemical | ChemComp-CA / |
---|---|
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-TRS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9828 Å |
Detector | Type: THOMSON/PRINCETON / Detector: CCD / Date: Feb 28, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9828 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.28 Å / Num. all: 43621 / Num. obs: 43621 / % possible obs: 82.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4168 / % possible all: 54.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1AQH Resolution: 1.8→44.28 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Following residues have been refined in double conformations: Arg 49, Thr 96, Ser 102, Arg 234, Arg 282, Arg 373, Val 420
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→44.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|