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Yorodumi- PDB-3iiz: X-ray structure of the FeFe-hydrogenase maturase HydE from T. mar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iiz | ||||||
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Title | X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with S-adenosyl-L-methionine | ||||||
Components | Biotin synthetase, putative | ||||||
Keywords | ADOMET BINDING PROTEIN / Adomet radical / SAM radical / HYDE / hydrogenase / Fe4S4 cluster / adomet cleavage / maturation / adenosylmethionine | ||||||
Function / homology | Function and homology information water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / organic cyclic compound biosynthetic process / 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 / organic cyclic compound biosynthetic process / 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: 1.62 Å | ||||||
Authors | Nicolet, Y. / Amara, P. / Mouesca, J.M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins Authors: Nicolet, Y. / Amara, P. / Mouesca, J.-M. / 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 | 3iiz.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iiz.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/3iiz ftp://data.pdbj.org/pub/pdb/validation_reports/ii/3iiz | HTTPS FTP |
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-Related structure data
Related structure data | 3iixC 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: 39889.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_1269 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9X0Z6 |
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-Non-polymers , 8 types, 459 molecules
#2: Chemical | ChemComp-SF4 / | ||||||||||
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#3: Chemical | ChemComp-SAM / | ||||||||||
#4: Chemical | ChemComp-CPS / #5: Chemical | ChemComp-FES / | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CO3 / | #9: 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: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, LISO4, TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-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 4 / Detector: CCD / Date: Jun 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→43 Å / Num. obs: 41143 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.39 |
Reflection shell | Resolution: 1.62→1.72 Å / Redundancy: 1.45 % / Mean I/σ(I) obs: 2.38 / Num. unique all: 13887 / Rsym value: 0.369 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CIW Resolution: 1.62→38.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.665 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The Friedel mates have been separated during data processing to extract the anomalous signal.
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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: 12.188 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→38.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20
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