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Yorodumi- PDB-1nbo: The dual coenzyme specificity of photosynthetic glyceraldehyde-3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nbo | ||||||
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Title | The dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD | ||||||
Components | glyceraldehyde-3-phosphate dehydrogenase A | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Dual Coenzyme Specificity of Photosynthetic Glyceraldehyde-3-phosphate Dehydrogenase Interpreted by the Crystal Structure of A(4) Isoform Complexed with NAD Authors: Falini, G. / Fermani, S. / Ripamonti, A. / Sabatino, P. / Sparla, F. / Pupillo, P. / Trost, P. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure Of The Non-Regulatory A4 Isoform Of Spinach Chloroplast Glyceraldehyde-3-Phosphate Dehydrogenase Complexed With Nadp Authors: Fermani, S. / Ripamonti, A. / Sabatino, P. / Zanotti, G. / Scagliarini, S. / Sparla, F. / Trost, P. / Pupillo, P. #2: Journal: J.Biol.Chem. / Year: 2002 Title: The C-terminal extension of glyceraldehyde-3-phosphate dehydrogenase subunit B acts as an autoinhibitory domain regulated by thioredoxins and nicotinamide adenine dinucleotide Authors: Sparla, F. / Pupillo, P. / Trost, P. #3: Journal: Biochim.Biophys.Acta / Year: 1990 Title: Chloroplast glyceraldehyde-3-phosphate dehydrogenase (NADP): amino acid sequence of the subunits from isoenzyme I and structural relationship with isoenzyme II Authors: Ferri, G. / Stoppini, M. / Meloni, M. / Zapponi, M.C. / Iadarola, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbo.cif.gz | 214.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbo.ent.gz | 171.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbo_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1nbo_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1nbo_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 1nbo_validation.cif.gz | 62.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbo ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbo | HTTPS FTP |
-Related structure data
Related structure data | 1jn0S S: Starting model for refinement |
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Similar 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 the monomer in the asymmetric unit by the operations: -x, y, 2-z and x, 1-y, 2-z and -x, 1-y, z or generated from the dimer in the asymmetric unit by the two fold axis: 1/2-x, 3/2-y, z. |
-Components
#1: Protein | Mass: 36256.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: GapA / Organ: leaves / Organelle: Chloroplast / Plasmid: pET-28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P19866, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.2 Å3/Da / Density % sol: 61.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate 2 M, Tris-HCl, 0.1 M, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.6→90 Å / Num. all: 45974 / Num. obs: 43213 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 26 | ||||||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 9.3 / Rsym value: 0.201 / % possible all: 99.9 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 90 Å / Num. obs: 43271 / Num. measured all: 679015 | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JN0 Resolution: 2.6→77.2 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.0324 Å2 / ksol: 0.371898 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→77.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.203 |