+Open data
-Basic information
Entry | Database: PDB / ID: 2yyy | ||||||
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Title | Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Glyceraldehyde 3-phosphate binding / Alpha and beta proteins (a/b) class / MJ1146 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) / 4-hydroxy-tetrahydrodipicolinate reductase / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lysine biosynthetic process via diaminopimelate / glycolytic process / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Malay, A.D. / Bessho, Y. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii. Authors: Malay, A.D. / Bessho, Y. / Ellis, M.J. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S. / Shinkai, A. / Padmanabhan, B. / Yokoyama, S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yyy.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yyy.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yyy_validation.pdf.gz | 538 KB | Display | wwPDB validaton report |
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Full document | 2yyy_full_validation.pdf.gz | 544.6 KB | Display | |
Data in XML | 2yyy_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2yyy_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyy ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyy | HTTPS FTP |
-Related structure data
Related structure data | 1cf2S 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: 38149.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM2661 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q58546, glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 293 K / Method: oil-batch / pH: 8.5 Details: 0.2M magnesium chloride hexahydrate, 0.08M tris hydrochloride, pH 8.5, 24%(w/v) PEG4000, 20%(v/v) glycerol anhydrous, oil-batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: double crystal monochromator with sagittal focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.117 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 64389 / Num. obs: 62507 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.238 / Num. unique all: 4944 / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CF2 Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.612 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.797 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.898 Å / Total num. of bins used: 20 /
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