+Open data
-Basic information
Entry | Database: PDB / ID: 3p13 | ||||||
---|---|---|---|---|---|---|---|
Title | Complex Structure of D-ribose Pyranase Sa240 with D-ribose | ||||||
Components | D-ribose pyranase | ||||||
Keywords | ISOMERASE / RbsD / D-ribose Pyranase / Sa240 / Carbohydrate metabolism | ||||||
Function / homology | Function and homology information intramolecular transferase activity / D-ribose pyranase / D-ribose pyranase activity / intramolecular lyase activity / D-ribose catabolic process / monosaccharide binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Wu, M. / Wang, L. / Zang, J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Crystal structure of Sa240: A ribose pyranase homolog with partial active site from Staphylococcus aureus Authors: Wang, L. / Wu, M. / Zang, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3p13.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3p13.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 3p13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p13_validation.pdf.gz | 472 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3p13_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 3p13_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 3p13_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/3p13 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/3p13 | HTTPS FTP |
-Related structure data
Related structure data | 3p12SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16443.842 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: rbsD, SAOUHSC_00240 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q2G1A5, Isomerases; Intramolecular lyases #2: Sugar | ChemComp-RIP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate pH 4.6, 2.0M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 31573 / Num. obs: 30275 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.08 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1527 / Rsym value: 0.402 / % possible all: 96.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P12 Resolution: 2.35→45.65 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R Free: 0.235 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.993 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→45.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
|