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Yorodumi- PDB-3iix: X-ray structure of the FeFe-hydrogenase maturase HydE from T. mar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iix | |||||||||
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Title | X-ray structure of the FeFe-hydrogenase maturase HydE from T. maritima in complex with methionine and 5'deoxyadenosine | |||||||||
Components | [FeFe] hydrogenase maturase subunit HydE | |||||||||
Keywords | ADOMET BINDING PROTEIN / ADOMET RADICAL / SAM RADICAL / ADOMET CLEAVAGE / FE4S4 CLUSTER / HYDE / HYDROGENASE / MATURATION / BETA BARREL / DEOXYADENOSINE | |||||||||
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 MSB8 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 3iix.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iix.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 3iix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/3iix ftp://data.pdbj.org/pub/pdb/validation_reports/ii/3iix | HTTPS FTP |
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-Related structure data
Related structure data | 3iizC 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: 39937.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1269, THEMA_07990, Tmari_1274 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors |
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-Non-polymers , 8 types, 479 molecules
#2: Chemical | ChemComp-SF4 / | ||||||||
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#3: Chemical | ChemComp-MET / | ||||||||
#4: Chemical | ChemComp-5AD / | ||||||||
#5: Chemical | ChemComp-CPS / #6: Chemical | ChemComp-S3H / | #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: 2.18 Å3/Da / Density % sol: 43.47 % |
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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: ID29 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→58.22 Å / Num. obs: 88534 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.045 / Net I/σ(I): 14.87 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 1.46 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 31571 / Rsym value: 0.407 / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CIW Resolution: 1.25→58.22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.439 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.043 / 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: 11.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→58.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.251→1.283 Å / Total num. of bins used: 20
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