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Yorodumi- PDB-1q4n: Structural studies of Phe256Trp of human salivary alpha-amylase: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q4n | |||||||||
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Title | Structural studies of Phe256Trp of human salivary alpha-amylase: implications for the role of a conserved water molecule and its associated chain in enzyme activity | |||||||||
Components | Alpha-amylase, salivary | |||||||||
Keywords | HYDROLASE / AMYLASE / MUTAGENESIS / TRIS / INHIBITOR | |||||||||
Function / homology | Function and homology information Digestion of dietary carbohydrate / oligosaccharide metabolic process / alpha-amylase / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Ramasubbu, N. | |||||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2004 Title: Structural studies of a Phe256Trp mutant of human salivary alpha-amylase: implications for the role of a conserved water molecule in enzyme activity Authors: Ramasubbu, N. / Sundar, K. / Ragunath, C. / Rafi, M.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4n.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4n.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4n ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4n | HTTPS FTP |
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-Related structure data
Related structure data | 1mfvS 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: 55994.297 Da / Num. of mol.: 1 / Mutation: F256W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMY1A OR AMY1 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-TAM / |
#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: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9 Details: MPD, Calcium Chloride, Tris, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 100K |
Crystal grow | *PLUS Method: unknown / Details: Ramasubbu, N., (1991) Proteins, 11, 230. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2001 / 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: 2.07→41.1 Å / Num. all: 89732 / Num. obs: 30610 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.07→2.14 Å / % possible all: 60 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Redundancy: 3 % / Num. measured all: 89732 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 60 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MFV Resolution: 2.07→41.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.831 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.17 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.753 Å2
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Refine analyze | Luzzati coordinate error obs: 0.216 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.124 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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