[English] 日本語
![](img/lk-miru.gif)
- PDB-8v2t: Phosphoheptose isomerase GMHA from Burkholderia pseudomallei boun... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8v2t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Phosphoheptose isomerase GMHA from Burkholderia pseudomallei bound to inhibitor Mut148591 | |||||||||
![]() | Phosphoheptose isomerase | |||||||||
![]() | ISOMERASE/INHIBITOR / heptose biosynthesis / ISOMERASE-INHIBITOR complex | |||||||||
Function / homology | ![]() D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / capsule polysaccharide biosynthetic process / carbohydrate derivative binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Junop, M.S. / Brown, C. / Szabla, R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria. Authors: Moreau, F. / Atamanyuk, D. / Blaukopf, M. / Barath, M. / Herczeg, M. / Xavier, N.M. / Monbrun, J. / Airiau, E. / Henryon, V. / Leroy, F. / Floquet, S. / Bonnard, D. / Szabla, R. / Brown, C. ...Authors: Moreau, F. / Atamanyuk, D. / Blaukopf, M. / Barath, M. / Herczeg, M. / Xavier, N.M. / Monbrun, J. / Airiau, E. / Henryon, V. / Leroy, F. / Floquet, S. / Bonnard, D. / Szabla, R. / Brown, C. / Junop, M.S. / Kosma, P. / Gerusz, V. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 94.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v4jC ![]() 2x3yS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23393.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: K96423 / Gene: gmhA / Plasmid: pNIC28-Bsa4 Details (production host): gmhA gene cloned into pNIC28-Bsa4 plasmid backbone Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 222 molecules ![](data/chem/img/XLR.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-XLR / |
---|---|
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 33.08 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1 uL protein solution (10 mg/mL GmhA, 500 mM sodium chloride, 10 mM HEPES, pH 7.0) + crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) suspended over 1.5 M ammonium ...Details: 1 uL protein solution (10 mg/mL GmhA, 500 mM sodium chloride, 10 mM HEPES, pH 7.0) + crystallization solution (10% w/v PEG4000, 0.1 M sodium acetate, pH 4.6) suspended over 1.5 M ammonium sulfate. Once crystals were grown, 0.2 uL ligand solution (50 mM Mut148591, 50 mM HEPES, pH 7.5) was added to the drops and allowed to soak for 90 minutes. Temp details: Incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.402→39.06 Å / Num. obs: 34849 / % possible obs: 99.64 % / Redundancy: 12 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06467 / Rpim(I) all: 0.01944 / Rrim(I) all: 0.06761 / Net I/σ(I): 21.23 |
Reflection shell | Resolution: 1.402→1.452 Å / Redundancy: 10 % / Rmerge(I) obs: 0.4377 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 3323 / CC1/2: 0.946 / CC star: 0.986 / Rpim(I) all: 0.1396 / Rrim(I) all: 0.4607 / % possible all: 96.54 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2X3Y Resolution: 1.402→39.06 Å / SU ML: 0.1263 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.7947 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.402→39.06 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|