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Yorodumi- PDB-1qhp: FIVE-DOMAIN ALPHA-AMYLASE FROM BACILLUS STEAROTHERMOPHILUS, MALTO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qhp | |||||||||
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Title | FIVE-DOMAIN ALPHA-AMYLASE FROM BACILLUS STEAROTHERMOPHILUS, MALTOSE COMPLEX | |||||||||
Components | ALPHA-AMYLASE | |||||||||
Keywords | HYDROLASE / AMYLASE / GLYCOSIDE HYDROLASE / STARCH DEGRADATION | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltohydrolase / glucan 1,4-alpha-maltohydrolase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Dauter, Z. / Dauter, M. / Brzozowski, A.M. / Christensen, S. / Borchert, T.V. / Beier, L. / Wilson, K.S. / Davies, G.J. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution. Authors: Dauter, Z. / Dauter, M. / Brzozowski, A.M. / Christensen, S. / Borchert, T.V. / Beier, L. / Wilson, K.S. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qhp.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qhp.ent.gz | 135.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qhp ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qhp | HTTPS FTP |
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-Related structure data
Related structure data | 1qhoC 1cdgS 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
#1: Protein | Mass: 75214.812 Da / Num. of mol.: 1 / Fragment: INTACT PROTEIN, ALL 5 DOMAINS Source method: isolated from a genetically manipulated source Details: MALTOSE CONTAINING Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Bacillus subtilis (bacteria) References: UniProt: P19531, glucan 1,4-alpha-maltohydrolase | ||||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 19 MG ML-1 ENZYME IN 10MM TRIS-HCL BUFFER PH 6.0, 0.2M NACL, 5MM CACL2. THE WELL SOLUTION CONTAINED 0.9M LI2SO4, 2.5% PEH 1450, 50MM TEA BUFFER (PH 6.5) AND 100MM MALTOSE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of 1:1 mixture of well and protein solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: LONG FOCUSSING MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 460513 / % possible obs: 95.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Rsym value: 8 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / Rsym value: 45 / % possible all: 92.5 |
Reflection | *PLUS Num. obs: 87912 / Num. measured all: 460513 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CDG Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.278 / Rfactor Rwork: 0.225 |