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Yorodumi- PDB-1h17: Pyruvate Formate-Lyase (E.coli) in complex with CoA and the subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h17 | ||||||
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Title | Pyruvate Formate-Lyase (E.coli) in complex with CoA and the substrate analog oxamate | ||||||
Components | FORMATE ACETYLTRANSFERASE 1 | ||||||
Keywords | TRANSFERASE / LYASE / GLYCYL RADICAL ENZYME / ACYLTRANSFERASE ACETYLATION | ||||||
Function / homology | Function and homology information formate C-acetyltransferase / formate C-acetyltransferase activity / glucose metabolic process / membrane / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Becker, A. / Kabsch, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical for Pyruvate Cleavage Authors: Becker, A. / Kabsch, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h17.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h17.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h17_validation.pdf.gz | 655.1 KB | Display | wwPDB validaton report |
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Full document | 1h17_full_validation.pdf.gz | 667.7 KB | Display | |
Data in XML | 1h17_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1h17_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h17 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h17 | HTTPS FTP |
-Related structure data
Related structure data | 1h16C 1h18C 3pflS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 85327.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEX OF PYRUVATE FORMATE-LYASE WITH SUBSTRATE COA AND THE SUBSTRATE ANALOG OXAMATE Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P09373, formate C-acetyltransferase |
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-Non-polymers , 7 types, 1282 molecules
#2: Chemical | ChemComp-COA / | ||||||||
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#3: Chemical | ChemComp-OXM / | ||||||||
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Chemical | #8: 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: 2.54 Å3/Da / Density % sol: 51.54 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.3 / Details: pH 7.30 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOT/ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / 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→15 Å / Num. obs: 86622 / % possible obs: 98.5 % / Redundancy: 6.89 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.77 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 5.03 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.83 / % possible all: 94 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 596858 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PFL Resolution: 1.75→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5320444.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: ONLY A PART (C8 H18 O5) OF THE POLYETHYLENE MOLECULE 5000 MOMOMETHYL ETHER COULD BE SEEN IN THE ELECTRON DENSITY MAP.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.2656 Å2 / ksol: 0.373702 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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