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Yorodumi- PDB-1qb4: CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qb4 | ||||||
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Title | CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE | ||||||
Components | PHOSPHOENOLPYRUVATE CARBOXYLASE | ||||||
Keywords | LYASE / ALPHA BETA BARREL | ||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / carbon fixation / oxaloacetate metabolic process / tricarboxylic acid cycle / gluconeogenesis / protein homotetramerization / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Matsumura, H. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Izui, K. / Kai, Y. | ||||||
Citation | Journal: FEBS Lett. / Year: 1999 Title: Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli Authors: Matsumura, H. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Izui, K. / Kai, Y. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Three-dimensional Structure of Phosphoenolpyruvate Carboxylase: A proposed mechanism for allosteric inhibition Authors: Kai, Y. / Matsumura, H. / Inoue, T. / Terada, K. / Nagara, Y. / Yoshinaga, T. / Kihara, A. / Tsumura, K. / Izui, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qb4.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qb4.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qb4 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qb4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a tetramer. |
-Components
#1: Protein | Mass: 99175.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Production host: Escherichia coli (E. coli) References: UniProt: P00864, phosphoenolpyruvate carboxylase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ASP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.01 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 300, MANGANESE SULPHATE, SUCROSE., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 34597 / Num. obs: 34589 / % possible obs: 90.9 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 4.56 % / Biso Wilson estimate: 42.832 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.249 / Num. unique all: 3145 / % possible all: 83.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 34597 / % possible obs: 90.7 % / Num. measured all: 157727 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / σ(F): 0.5 / σ(I): 0.5
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |