[English] 日本語
Yorodumi- PDB-3f7t: Structure of active IspH shows a novel fold with a [3Fe-4S] clust... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f7t | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of active IspH shows a novel fold with a [3Fe-4S] cluster in the catalytic centre | ||||||
Components | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / pseudo-C3-symmetry / unprecedent fold for FeS-cluster proteins / Iron / Iron-sulfur / Isoprene biosynthesis / Metal-binding / NADP / PROTEIN BINDING | ||||||
Function / homology | Function and homology information hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Graewert, T. / Eppinger, J. / Rohdich, F. / Bacher, A. / Eisenreich, W. / Groll, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 Title: Structure of active IspH enzyme from Escherichia coli provides mechanistic insights into substrate reduction. Authors: Grawert, T. / Rohdich, F. / Span, I. / Bacher, A. / Eisenreich, W. / Eppinger, J. / Groll, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f7t.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f7t.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f7t_validation.pdf.gz | 484.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f7t_full_validation.pdf.gz | 497.2 KB | Display | |
Data in XML | 3f7t_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 3f7t_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/3f7t ftp://data.pdbj.org/pub/pdb/validation_reports/f7/3f7t | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 1 - 310 / Label seq-ID: 13 - 322
| ||||||||||||||||||
Details | Asymmetric unit contains two biological assemblies; IspH protein is monomeric |
-Components
#1: Protein | Mass: 36223.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: cytosolic protein / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0029, ispH, JW0027, lytB, yaaE / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.87 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0,1.7368 | |||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2007 / Details: SILICON OPTICS | |||||||||
Radiation | Monochromator: double bounce Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.8→40 Å / Num. all: 78209 / Num. obs: 78209 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 35.16 Å2 / Rmerge(I) obs: 0.075 | |||||||||
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10654 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.419 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.117 / ESU R Free: 0.118 / 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: 35.156 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2390 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|