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Yorodumi- PDB-4jxc: X-ray snapshots of possible intermediates in the time course of s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jxc | ||||||
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Title | X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters | ||||||
Components | FEFE-HYDROGENASE MATURASE | ||||||
Keywords | OXIDOREDUCTASE / Radical SAM Protein / FeFe-hydrogenase active site Assembly / Fe4S4 cluster / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information water-soluble vitamin biosynthetic process / sulfur compound biosynthetic process / : / : / Oxidoreductases; Acting on a sulfur group of donors / : / 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: 1.5 Å | ||||||
Authors | Nicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters. Authors: Nicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jxc.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jxc.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jxc_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4jxc_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4jxc_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4jxc_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jxc ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jxc | HTTPS FTP |
-Related structure data
Related structure data | 4jy8C 4jy9C 4jydC 4jyeC 4jyfC 3ciwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1269, ThemaDRAFT_0043 / Plasmid: pHydE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0Z6 |
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-Non-polymers , 10 types, 343 molecules
#2: Chemical | ChemComp-SF4 / | ||||||||||||||
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#3: Chemical | ChemComp-SAM / | ||||||||||||||
#4: Chemical | ChemComp-1N7 / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-FES / | #7: Chemical | #8: Chemical | ChemComp-IPA / | #9: Chemical | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 200 mM Li2SO4, 30% PEG 4000, Anaerobic chamber (N2/H2 95/5%) , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2005 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→60 Å / Num. all: 119182 / Num. obs: 101819 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.45→1.54 Å / % possible all: 88.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CIW Resolution: 1.5→58.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.316 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 10.767 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→58.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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