+Open data
-Basic information
Entry | Database: PDB / ID: 1vbh | ||||||
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Title | Pyruvate Phosphate Dikinase with bound Mg-PEP 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 | 1vbh.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbh.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vbh_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 1vbh_full_validation.pdf.gz | 490.7 KB | Display | |
Data in XML | 1vbh_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 1vbh_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbh ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbh | HTTPS FTP |
-Related structure data
Related structure data | 1vbgSC S: Starting model for refinement C: citing same article (ref.) |
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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 | ChemComp-SO4 / |
#4: Chemical | ChemComp-PEP / |
#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: 3.2 Å3/Da / Density % sol: 61.22 % |
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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: BL45PX / Wavelength: 1.02 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 12, 2000 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.63 Å / Num. all: 51442 / Num. obs: 51391 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.04 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.3→2.44 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VBG Resolution: 2.3→45.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 76298.87 / 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: 37.6024 Å2 / ksol: 0.341708 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→45.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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