[English] 日本語
![](img/lk-miru.gif)
- PDB-6nau: 1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolac... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6nau | ||||||
---|---|---|---|---|---|---|---|
Title | 1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae | ||||||
![]() | 6-phosphogluconolactonase | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phosphogluconolactonase | ||||||
Function / homology | ![]() 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / glucose metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Pshenychnyi, S. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae. Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 262.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 207.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 57.3 KB | Display | |
Data in CIF | ![]() | 92.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dt3C ![]() 6duxC ![]() 6dvvC ![]() 6dxnC ![]() 6e85C ![]() 6nbgC ![]() 6ndiC ![]() 6wn5C ![]() 6wn8C ![]() 6x1lC ![]() 7rjjC ![]() 7tl5C ![]() 7tzpC ![]() 4qrjS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36462.789 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ybhE, pgl, NCTC9504_04578 / Plasmid: pMCSG53 Production host: ![]() ![]() References: UniProt: A0A2X3FDC7, UniProt: A6T6J6*PLUS, 6-phosphogluconolactonase #2: Chemical | ChemComp-B3P / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3, Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 138516 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.035 / Rrim(I) all: 0.106 / Rsym value: 0.1 / Χ2: 1.005 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 6923 / CC1/2: 0.861 / Rpim(I) all: 0.258 / Rrim(I) all: 0.757 / Rsym value: 0.711 / Χ2: 1 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4QRJ Resolution: 1.55→29.33 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.283 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.521 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.55→29.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|