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Yorodumi- PDB-1qwg: Crystal structure of Methanococcus jannaschii phosphosulfolactate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qwg | ||||||
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Title | Crystal structure of Methanococcus jannaschii phosphosulfolactate synthase | ||||||
Components | (2R)-phospho-3-sulfolactate synthase | ||||||
Keywords | LYASE / beta-alpha-barrel | ||||||
Function / homology | Function and homology information phosphosulfolactate synthase / coenzyme M biosynthetic process / phosphosulfolactate synthase activity / sulfopyruvate decarboxylase activity Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Wise, E.L. / Graham, D.E. / White, R.H. / Rayment, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase Authors: Wise, E.L. / Graham, D.E. / White, R.H. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qwg.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qwg.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qwg_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 1qwg_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 1qwg_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1qwg_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/1qwg ftp://data.pdbj.org/pub/pdb/validation_reports/qw/1qwg | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: Protein | ( Mass: 28407.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: ComA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q57703, Lyases; Carbon-sulfur lyases | ||
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#2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 43.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 1.6 M Ammonium sulfate, 100 mM succinate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→90 Å / Num. all: 29827 / Num. obs: 29827 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.28 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.7 / % possible all: 56.8 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 31689 / Num. measured all: 446003 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 68.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→65.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.744 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: Engh & Huber
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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: 18.062 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→65.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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