+Open data
-Basic information
Entry | Database: PDB / ID: 1vbg | ||||||
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Title | Pyruvate Phosphate Dikinase from Maize | ||||||
Components | pyruvate,orthophosphate dikinase | ||||||
Keywords | TRANSFERASE / Maize / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / photosynthesis / chloroplast / kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nakanishi, T. / Nakatsu, T. / Matsuoka, M. / Sakata, K. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion Authors: Nakanishi, T. / Nakatsu, T. / Matsuoka, M. / Sakata, K. / Kato, H. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize Authors: Nakanishi, T. / Ohki, Y. / Oda, J. / Matsuoka, M. / Sakata, K. / Kato, H. #2: Journal: J.BIOL.CHEM. / Year: 1988 Title: Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence Authors: Matsuoka, M. / Ozeki, Y. / Yamamoto, N. / Hirano, H. / Kano-Murakami, Y. / Tanaka, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbg.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbg.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 1vbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vbg_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 1vbg_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 1vbg_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 1vbg_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbg ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbg | HTTPS FTP |
-Related structure data
Related structure data | 1vbhC 1dikS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 95294.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P11155, pyruvate, phosphate dikinase | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: 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: 3.04 Å3/Da / Density % sol: 59.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, magnesium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→73.29 Å / Num. all: 51097 / Num. obs: 51096 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.65 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DIK Resolution: 2.3→46.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2321429.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5055 Å2 / ksol: 0.365817 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→46.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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