[English] 日本語
Yorodumi- PDB-5f1v: biomimetic design results in a potent allosteric inhibitor of dih... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f1v | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | biomimetic design results in a potent allosteric inhibitor of dihydrodipicolinate synthase from Campylobacter jejuni | ||||||||||||
Components | 4-hydroxy-tetrahydrodipicolinate synthaseDihydrodipicolinate synthase | ||||||||||||
Keywords | LYASE/LYASE inhibitor / schiff-base / aldolase / TIM barrel / LYASE-LYASE inhibitor complex | ||||||||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Conly, C.J.T. / Palmer, D.R.J. / Sanders, D.A.R. | ||||||||||||
Funding support | Canada, 1items
| ||||||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni. Authors: Skovpen, Y.V. / Conly, C.J. / Sanders, D.A. / Palmer, D.R. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5f1v.cif.gz | 472 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5f1v.ent.gz | 387.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1v ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1v | HTTPS FTP |
---|
-Related structure data
Related structure data | 5f1uC 3lerS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32648.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: dapA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase |
---|
-Non-polymers , 5 types, 418 molecules
#2: Chemical | ChemComp-3VN / ( #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | Authors state that in ligand 3VN, carbonyl groups are de-protonated, and amine groups are protonated. |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 16% PEG 4000, 0.2 M NaAct, 0.1 mM TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9798 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 1, 2013 |
Radiation | Monochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 59651 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 1.34 % / Biso Wilson estimate: 22.62 Å2 / Rmerge F obs: 0.983 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.397 / Χ2: 1.015 / Net I/σ(I): 11.79 / Num. measured all: 1110812 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge F obs: 0.034 / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 3.44 / Num. measured obs: 13656 / Num. possible: 38523 / Num. unique obs: 7716 / Rrim(I) all: 24.807 / Rejects: 0 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LER Resolution: 2.2→48.47 Å / FOM work R set: 0.9035 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.85 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.13 Å2 / Biso mean: 24.6 Å2 / Biso min: 10.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 6.3131 Å / Origin y: 3.3139 Å / Origin z: 18.5231 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|