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Yorodumi- PDB-3pfl: CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pfl | ||||||
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Title | CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE | ||||||
Components | PROTEIN (FORMATE ACETYLTRANSFERASE 1) | ||||||
Keywords | LYASE/TRANSFERASE / GLYCYL RADICAL ENZYME / TRANSFERASE / GLUCOSE METABOLISM / LYASE-TRANSFERASE COMPLEX | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Becker, A. / Fritz-Wolf, K. / Kabsch, W. / Knappe, J. / Schultz, S. / Wagner, A.F.V. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase. Authors: Becker, A. / Fritz-Wolf, K. / Kabsch, W. / Knappe, J. / Schultz, S. / Volker Wagner, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pfl.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pfl.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/3pfl ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pfl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9119, 0.4058, 0.061), Vector: |
-Components
#1: Protein | Mass: 85327.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P09373, formate C-acetyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.3 / Details: pH 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8467 |
Detector | Type: MARRESEARCH / Date: Feb 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8467 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 61282 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.088 |
Reflection | *PLUS Num. measured all: 333383 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 626424.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: DISORDERED REGIONS (RESIDUES A1-A3 AND B1-B3) WERE MODELED STEREOCHEMICALLY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.33 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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