[English] 日本語
Yorodumi- PDB-3cix: X-RAY structure of the [FeFe]-hydrogenase maturase HydE from ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cix | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY structure of the [FeFe]-hydrogenase maturase HydE from thermotoga maritima in complex with thiocyanate | ||||||
Components | FeFe-Hydrogenase maturase | ||||||
Keywords | ADOMET BINDING PROTEIN / Radical AdoMet Protein / FeFe-Hydrogenase maturation / Beta barrel / Fe4S4 cluster / Thiocyanate / Fe2S2 cluster | ||||||
Function / homology | Function and homology information water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Nicolet, Y. / Ruback, J.K. / Posewitz, M.C. / Amara, P. / Mathevon, C. / Atta, M. / Fontecave, M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: X-ray Structure of the [FeFe]-Hydrogenase Maturase HydE from Thermotoga maritima Authors: Nicolet, Y. / Rubach, J.K. / Posewitz, M.C. / Amara, P. / Mathevon, C. / Atta, M. / Fontecave, M. / Fontecilla-Camps, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3cix.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3cix.ent.gz | 137.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cix ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cix | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ciwSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39873.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HydE / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9X0Z6 |
---|
-Non-polymers , 10 types, 380 molecules
#2: Chemical | ChemComp-SCN / | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-SF4 / | #5: Chemical | ChemComp-SAH / | #6: Chemical | ChemComp-CPS / #7: Chemical | ChemComp-SAT / | #8: Chemical | ChemComp-FES / | #9: Chemical | ChemComp-PEG / | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000 35%, 100mM TrisHCl, pH8.5, 100mM LiSO4, 3mM CHAPS, 20mg/mL Protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→58.52 Å / Num. obs: 37499 / % possible obs: 95.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4270 / % possible all: 77.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CIW Resolution: 1.7→32.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.936 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.102 / 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: 13.913 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→32.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|