[English] 日本語
Yorodumi- PDB-1ro7: Structural analysis of the sialyltransferase CstII from Campyloba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ro7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analogue, CMP-3FNeuAc. | ||||||
Components | alpha-2,3/8-sialyltransferase | ||||||
Keywords | TRANSFERASE / mixed alpha/beta / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog. Authors: Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ro7.cif.gz | 216.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ro7.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 1ro7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/1ro7 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/1ro7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30730.379 Da / Num. of mol.: 4 / Mutation: I53S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cst / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LAK3, EC: 2.4.99.- #2: Chemical | ChemComp-MPD / ( | #3: Chemical | ChemComp-CSF / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.62 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG MME 2000, sodium chloride, bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 99748 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.526 / % possible all: 98.5 |
Reflection | *PLUS % possible obs: 99.6 % / Num. measured all: 429958 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.526 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.64 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1876668.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.0095 Å2 / ksol: 0.338876 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|