[English] 日本語
Yorodumi- PDB-3m07: 1.4 Angstrom Resolution Crystal Structure of Putative alpha Amyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m07 | ||||||
---|---|---|---|---|---|---|---|
Title | 1.4 Angstrom Resolution Crystal Structure of Putative alpha Amylase from Salmonella typhimurium. | ||||||
Components | Putative alpha amylase | ||||||
Keywords | UNKNOWN FUNCTION / putative alpha amylase / idp00968 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase / 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity / trehalose biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.4 Angstrom Resolution Crystal Structure of Putative alpha Amylase from Salmonella typhimurium. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3m07.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3m07.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 3m07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m07_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3m07_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 3m07_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 3m07_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/3m07 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/3m07 | HTTPS FTP |
-Related structure data
Related structure data | 2bhzS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68587.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: NP_460519, STM1560 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZPF0 |
---|
-Non-polymers , 6 types, 630 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-BTB / | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.73 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein solution: 8.1 mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen solution: JCSG+, H11, 0.2M Magnesium chloride, 0.1M bis-Tris (pH 5.5), 25% w/v PEG 3350., VAPOR DIFFUSION, ...Details: Protein solution: 8.1 mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen solution: JCSG+, H11, 0.2M Magnesium chloride, 0.1M bis-Tris (pH 5.5), 25% w/v PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2010 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 97228 / Num. obs: 97228 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4685 / % possible all: 96.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BHZ Resolution: 1.4→29.79 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.979 / SU ML: 0.039 / Isotropic thermal model: Refined Individually / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.269 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→29.79 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|