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Yorodumi- PDB-1jqo: Crystal structure of C4-form phosphoenolpyruvate carboxylase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jqo | ||||||
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Title | Crystal structure of C4-form phosphoenolpyruvate carboxylase from maize | ||||||
Components | phosphoenolpyruvate carboxylase | ||||||
Keywords | LYASE / BETA BARREL / Carbon dioxide fixation | ||||||
Function / homology | Function and homology information response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / carbon fixation / apoplast / photosynthesis / tricarboxylic acid cycle ...response to cytokinin / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / response to nitrate / leaf development / response to ammonium ion / carbon fixation / apoplast / photosynthesis / tricarboxylic acid cycle / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 1jqo.cif.gz | 358.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jqo.ent.gz | 291 KB | Display | PDB format |
PDBx/mmJSON format | 1jqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jqo_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 1jqo_full_validation.pdf.gz | 542.2 KB | Display | |
Data in XML | 1jqo_validation.xml.gz | 69.2 KB | Display | |
Data in CIF | 1jqo_validation.cif.gz | 92.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jqo ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jqo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer generated from dimer in the assymmetric unit by two fole axis. |
-Components
#1: Protein | Mass: 109436.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / Strain: B37 / Tissue: leaves References: UniProt: P04711, phosphoenolpyruvate carboxylase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, Tris-HCl, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 25, 1999 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 3→86.2 Å / Num. all: 266008 / Num. obs: 58078 / % possible obs: 80.4 % / Observed criterion σ(I): 7.4 / Rmerge(I) obs: 0.091 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.309 / % possible all: 57.7 |
Reflection | *PLUS Num. measured all: 266008 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→86.2 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.43 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.06 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→86.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree error: 0.026
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Refinement | *PLUS Highest resolution: 3 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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