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Yorodumi- PDB-1szj: STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1szj | ||||||
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Title | STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION | ||||||
Components | D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE / MOLECULAR SYMMETRY / ALLOSTERISM | ||||||
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 | Palinurus versicolor (painted spiny lobster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Song, S. / Li, J. / Lin, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1983 Title: Preliminary crystallographic studies of lobster D-glyceraldehyde-3-phosphate dehydrogenase and the modified enzyme carrying the fluorescent derivative. Authors: Song, S.Y. / Gao, Y.G. / Zhou, J.M. / Tsou, C.L. #1: Journal: Arch.Biochem.Biophys. / Year: 1993 Title: Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase from Palinurus Versicolor Carrying the Fluorescent Nad Derivatives at 2.7 A Resolution Authors: Lin, Z.J. / Li, J. / Zhang, F.M. / Song, S.Y. / Yang, J. / Liang, S.J. / Tsou, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1szj.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1szj.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 1szj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1szj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1szj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1szj_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 1szj_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/1szj ftp://data.pdbj.org/pub/pdb/validation_reports/sz/1szj | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99997, -0.00521, -0.0049), Vector: |
-Components
#1: Protein | Mass: 35767.004 Da / Num. of mol.: 2 / Fragment: NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN / Source method: isolated from a natural source / Details: COMPLEX WITH NAD+ Source: (natural) Palinurus versicolor (painted spiny lobster) Organ: TAIL / Tissue: TAIL MUSCLE References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (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: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62 % Description: THE 2.7 ANGSTROM STRUCTURE OF IRR-GAPDH FROM PALINURUS VERSICOLOR WAS DETERMINED BY MOLECULAR REPLACEMENT USING HOMARUS AMERICANUS HOLO-GAPDH AS A SEARCH MODEL. |
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Crystal grow | Temperature: 280 K / pH: 6.1 Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2. ...Details: THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULPHATE IN SAME BUFFER. THE CRYSTALLIZATION WAS CARRIED OUT AT 280K. |
-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 1, 1994 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 84900 / % possible obs: 83.5 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 1.6 / % possible all: 56.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMARUS AMERICANUS HOLO-GAPDH Resolution: 2→6 Å / Data cutoff low absF: 50 / σ(F): 3 Details: DURING THE REFINEMENT, NO NCS RESTRAINTS WERE USED.
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Displacement parameters | Biso mean: 32.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.09 Å
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Xplor file |
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