+Open data
-Basic information
Entry | Database: PDB / ID: 1w9x | |||||||||
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Title | Bacillus halmapalus alpha amylase | |||||||||
Components | ALPHA AMYLASE | |||||||||
Keywords | HYDROLASE / AMYLASE / ACARBOSE / BACILLUS / GLYCOSIDE HYDROLASE | |||||||||
Function / homology | Function and homology information alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | |||||||||
Biological species | BACILLUS HALMAPALUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Davies, G.J. / Brzozowski, A.M. / Dauter, Z. / Rasmussen, M.D. / Borchert, T.V. / Wilson, K.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of a Bacillus Halmapalus Family 13 Alpha-Amylase, Bha, in Complex with an Acarbose-Derived Nonasaccharide at 2.1 A Resolution Authors: Davies, G.J. / Brzozowski, A.M. / Dauter, Z. / Rasmussen, M.D. / Borchert, T.V. / Wilson, K.S. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w9x.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9x.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w9x_validation.pdf.gz | 662.7 KB | Display | wwPDB validaton report |
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Full document | 1w9x_full_validation.pdf.gz | 666.9 KB | Display | |
Data in XML | 1w9x_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 1w9x_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9x ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9x | HTTPS FTP |
-Related structure data
Related structure data | 1e3xS 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: 55276.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACARBOSE-DERIVED NONASACCHARIDE / Source: (gene. exp.) BACILLUS HALMAPALUS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: O82839*PLUS, alpha-amylase | ||||
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#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose Type: oligosaccharide / Mass: 1435.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #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: 2.57 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | pH: 7.5 Details: 30 MGML-1 IN 50 MM IMIDAZOLE, 5 MM CACL2, 25 MM ACARBOSE, PH 7.5 MIXED IN 1:1 RATIO WITH THE WELL SOLUTION CONSISTING OF 0.1 M IMIDAZOLE PH 7.5 100 MM MALTOSE, 5 MM CACL2, AND WITH 18% (W/V) ...Details: 30 MGML-1 IN 50 MM IMIDAZOLE, 5 MM CACL2, 25 MM ACARBOSE, PH 7.5 MIXED IN 1:1 RATIO WITH THE WELL SOLUTION CONSISTING OF 0.1 M IMIDAZOLE PH 7.5 100 MM MALTOSE, 5 MM CACL2, AND WITH 18% (W/V) MONOMETHYLETHER POLYETHYLENE GLYCOL 5K AS PRECIPITANT. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: 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: 2.1→15 Å / Num. obs: 30048 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E3X Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.781 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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