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Yorodumi- PDB-1jqn: Crystal structure of E.coli phosphoenolpyruvate carboxylase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jqn | ||||||
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Title | Crystal structure of E.coli phosphoenolpyruvate carboxylase in complex with Mn2+ and DCDP | ||||||
Components | phosphoenolpyruvate carboxylase | ||||||
Keywords | LYASE / BETA BARREL / Mn2+ and DCDP COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Matsumura, H. / Kai, Y. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases. Authors: Matsumura, H. / Xie, Y. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Ueno, Y. / Izui, K. / Kai, Y. #1: 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. #2: 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. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and preliminary x-ray diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize. Authors: Matsumura, H. / Nagata, T. / Terada, M. / Shirakata, S. / Inoue, T. / Yoshinaga, T. / Ueno, Y. / Saze, H. / Izui, K. / Kai, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jqn.cif.gz | 185 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jqn.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 1jqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jqn ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jqn | 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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Details | The biological assembly is a tetramer generated from monomer in the assymmetric unit by D2 symmetry. |
-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: Escherichia coli / Production host: Escherichia coli (E. coli) / Strain (production host): F15 References: UniProt: P00864, phosphoenolpyruvate carboxylase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ASP / |
#4: Chemical | ChemComp-DCO / |
#5: 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: 3.08 Å3/Da / Density % sol: 60.03 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG300, Tris-HCl, MnCl2, DCDP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 24, 1999 |
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: 2.35→39.5 Å / Num. all: 233027 / Num. obs: 45789 / % possible obs: 89.2 % / Observed criterion σ(I): 11.3 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.302 / % possible all: 61.9 |
Reflection | *PLUS Num. measured all: 233027 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.56 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.021
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.5 Å |