[English] 日本語
Yorodumi- PDB-1sfs: 1.07 A crystal structure of an uncharacterized B. stearothermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sfs | ||||||
---|---|---|---|---|---|---|---|
Title | 1.07 A crystal structure of an uncharacterized B. stearothermophilus protein | ||||||
Components | Hypothetical protein | ||||||
Keywords | Structural Genomics / unknown function / possible bacterial Lysozyme / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Rv2525c-like, glycoside hydrolase-like domain / Rv2525c-like, glycoside hydrolase-like domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION / Rbstp1166 protein Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.07 Å | ||||||
Authors | Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Moy, S.F. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: 1.07 A crystal structure of an uncharacterized B. stearothermophilus protein Authors: Minasov, G. / Brunzelle, J.S. / Shuvalova, L. / Moy, S.F. / Collart, F.R. / Anderson, W.F. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE RESIDUES 0 TO -23 ARE HIS TAG RESIDUES. THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN ...SEQUENCE RESIDUES 0 TO -23 ARE HIS TAG RESIDUES. THE SEQUENCE OF THE PROTEIN HAS NOT YET BEEN DEPOSITED IN ANY SEQUENCE REFERENCE DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sfs.cif.gz | 127 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sfs.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/1sfs ftp://data.pdbj.org/pub/pdb/validation_reports/sf/1sfs | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26965.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: RBSTP1166 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P84136 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M Ammonium Phosphate, 20% PEG, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→15 Å / Num. all: 90332 / Num. obs: 90332 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.53 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.24 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.64 / Num. unique all: 7244 / % possible all: 73.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 1.07→15 Å / Num. parameters: 22495 / Num. restraintsaints: 32495 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT
| |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.84 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 205 / Occupancy sum hydrogen: 1570.71 / Occupancy sum non hydrogen: 1975.72 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→15 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.07→1.11 Å
|