[English] 日本語
Yorodumi- PDB-3fax: The crystal structure of GBS pullulanase SAP in complex with malt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fax | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of GBS pullulanase SAP in complex with maltotetraose | |||||||||
Components | Reticulocyte binding protein | |||||||||
Keywords | HYDROLASE / TIM barrel / alpha amylase domain / pullulanase domain / Cell wall / Peptidoglycan-anchor / Secreted | |||||||||
Function / homology | Function and homology information Immunoglobulin-like - #1220 / Golgi alpha-mannosidase II / Glycosidases / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Streptococcus agalactiae COH1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Gourlay, L.J. | |||||||||
Citation | Journal: J.Bacteriol. / Year: 2009 Title: Group B Streptococcus pullulanase crystal structures in the context of a novel strategy for vaccine development Authors: Gourlay, L.J. / Santi, I. / Pezzicoli, A. / Grandi, G. / Soriani, M. / Bolognesi, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fax.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fax.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fax_validation.pdf.gz | 754.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3fax_full_validation.pdf.gz | 764 KB | Display | |
Data in XML | 3fax_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3fax_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3fax ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3fax | HTTPS FTP |
-Related structure data
Related structure data | 3fawSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 98557.578 Da / Num. of mol.: 1 Fragment: N2, N3, A and C pullulanase domains, UNP residues 346-1215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae COH1 (bacteria) Gene: SAN_1346 / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3DB05 | ||||
---|---|---|---|---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.8 Details: 30% PEG3K, 0.2M CaCl2, 0.05M CAPSO, pH9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 34193 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.064 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4926 / Rsym value: 0.351 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FAW Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.886 / SU B: 24.663 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.302 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.488 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|