+Open data
-Basic information
Entry | Database: PDB / ID: 2y8n | ||||||
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Title | Crystal structure of glycyl radical enzyme | ||||||
Components |
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Keywords | LYASE / RADICAL CHEMISTRY / METALLOENZYME / IRON-SULFUR CENTER | ||||||
Function / homology | Function and homology information 4-hydroxyphenylacetate decarboxylase / 4-hydroxyphenylacetate decarboxylase activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM SCATOLOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Martins, B.M. / Blaser, M. / Feliks, M. / Ullmann, G.M. / Selmer, T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 Title: Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme. Authors: Martins, B.M. / Blaser, M. / Feliks, M. / Ullmann, G.M. / Buckel, W. / Selmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y8n.cif.gz | 426.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y8n.ent.gz | 342.4 KB | Display | PDB format |
PDBx/mmJSON format | 2y8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/2y8n ftp://data.pdbj.org/pub/pdb/validation_reports/y8/2y8n | HTTPS FTP |
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-Related structure data
Related structure data | 2yajC 1r9dS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 100745.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM SCATOLOGENES (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS / Plasmid: PASK-IBA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA References: UniProt: Q38HX4, 4-hydroxyphenylacetate decarboxylase #2: Protein | Mass: 9353.634 Da / Num. of mol.: 2 / Fragment: NONE Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM SCATOLOGENES (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS / Plasmid: PASK-IBA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA References: UniProt: Q38HX3, 4-hydroxyphenylacetate decarboxylase #3: Chemical | ChemComp-SF4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 22 % PEG MME 550, 30 MM MGCL2, 100 MM TRIS/HCL PH 7.5 - 8.4 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→29.18 Å / Num. obs: 217979 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 17.09 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 5.7 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R9D Resolution: 1.75→29.184 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.98 / Stereochemistry target values: ML Details: FIRST 29 RESIDUES IN CHAINS A, C DISORDERED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.149 Å2 / ksol: 0.348 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→29.184 Å
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Refine LS restraints |
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LS refinement shell |
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