[English] 日本語
Yorodumi- PDB-1rqi: Active Conformation of Farnesyl Pyrophosphate Synthase Bound to I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqi | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate | |||||||||
Components | Geranyltranstransferase | |||||||||
Keywords | TRANSFERASE / isoprenyl synthase | |||||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / prenyltransferase activity / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | |||||||||
Authors | Hosfield, D.J. / Zhang, Y. / Dougan, D.R. / Brooun, A. / Tari, L.W. / Swanson, R.V. / Finn, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis Authors: Hosfield, D.J. / Zhang, Y. / Dougan, D.R. / Brooun, A. / Tari, L.W. / Swanson, R.V. / Finn, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rqi.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rqi.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rqi_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rqi_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 1rqi_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1rqi_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqi ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32268.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ISPA, B0421 / Production host: Escherichia coli (E. coli) References: UniProt: P22939, (2E,6E)-farnesyl diphosphate synthase |
---|
-Non-polymers , 5 types, 248 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DPO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
---|---|
Crystal grow | Temperature: 298 K / Method: nanoliter sitting drop vapor diffusion / pH: 6 Details: MPEG 2000, HEPES, pH 6, Nanoliter Sitting Drop Vapour Diffusion, temperature 298K |
Crystal grow | *PLUS Method: unknown / Details: Hosfield, D., (2003) J. Struct. Biol., 142, 207. |
-Data collection
Diffraction | Mean temperature: 97 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2002 / 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: 2.42→50 Å / Num. all: 27547 / Num. obs: 26473 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.1 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.42→2.51 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.44 / % possible all: 93.2 |
Reflection | *PLUS Num. measured all: 194920 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 93.2 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.67 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→43.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.369 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.461 / ESU R Free: 0.281 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.457 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→43.03 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.42→2.483 Å / Total num. of bins used: 20 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|