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Yorodumi- PDB-4fir: Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fir | ||||||
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Title | Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus | ||||||
Components | Pyridoxal biosynthesis lyase pdxS | ||||||
Keywords | LYASE / Pyrococcus horikoshii / pdxS / pyridoxal biosynthesis lyase / pyridoxal 5 -phosphate (PLP) | ||||||
Function / homology | Function and homology information pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Matsuura, A. / Yoon, J.Y. / Yoon, H.J. / Lee, H.H. / Suh, S.W. | ||||||
Citation | Journal: Mol.Cells / Year: 2012 Title: Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii. Authors: Matsuura, A. / Yoon, J.Y. / Yoon, H.J. / Lee, H.H. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fir.cif.gz | 377.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fir.ent.gz | 309.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/4fir ftp://data.pdbj.org/pub/pdb/validation_reports/fi/4fir | HTTPS FTP |
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-Related structure data
Related structure data | 4fiqC 1znnS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 37065.309 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: pdxS, PH1355 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: O59080, Lyases #2: Sugar | ChemComp-R5P / #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: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 297 K / pH: 8 Details: 100mM imidazole, 35% 2-methyl-2,4-pentanediol, 200mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 23, 2005 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 39532 / % possible obs: 98.5 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 3.1→3.15 Å / Rmerge(I) obs: 0.23 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZNN Resolution: 3.1→29.84 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.38 / Phase error: 23.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.27 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.21 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→29.84 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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