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Yorodumi- PDB-1cer: DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cer | ||||||
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Title | DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION | ||||||
Components | HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (ALDEHYDE(D)-NAD(A)) / GLYCOLYSIS / OXIDOREDUCTASE / NAD | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Tanner, J.J. / Hecht, R.M. / Krause, K.L. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution. Authors: Tanner, J.J. / Hecht, R.M. / Krause, K.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Preliminary Crystallographic Analysis of Glyceraldehyde-3-Phosphate Dehydrogenase from the Extreme Thermophile Thermus Aquaticus Authors: Tanner, J. / Hecht, R.M. / Pisegna, M. / Seth, D.M. / Krause, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cer.cif.gz | 489.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cer.ent.gz | 407 KB | Display | PDB format |
PDBx/mmJSON format | 1cer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cer_validation.pdf.gz | 952.8 KB | Display | wwPDB validaton report |
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Full document | 1cer_full_validation.pdf.gz | 1016.5 KB | Display | |
Data in XML | 1cer_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 1cer_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/1cer ftp://data.pdbj.org/pub/pdb/validation_reports/ce/1cer | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9965, 0.03559, 0.07567), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC SYMMETRY THAT GENERATES THE SECOND TETRAMER IN THE ASYMMETRIC UNIT. THIS APPROXIMATE TWO-FOLD ROTATION AROUND Z THAT GENERATES THE SECOND OF TWO TETRAMERS IN THE ASYMMETRIC UNIT. NOTE THAT THIS ENTRY CONTAINS ONLY ONE TETRAMER. | |
-Components
#1: Protein | Mass: 35941.273 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: THERMUS AQUATICUS GAPDH / Plasmid: PBR322 / Gene (production host): THERMUS AQUATICUS GAPDH / Production host: Escherichia coli (E. coli) / Strain (production host): W3CG References: UniProt: P00361, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 15, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Num. obs: 81628 / % possible obs: 72 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.0565 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 267328 / Rmerge(I) obs: 0.0565 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 30 % |
-Processing
Software |
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Refinement | Resolution: 2.5→12 Å / σ(F): 0
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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