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Yorodumi- PDB-1psd: THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1psd | ||||||
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Title | THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE | ||||||
Components | D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE (NAD(A)) | ||||||
Function / homology | Function and homology information 2-hydroxyglutarate dehydrogenase activity / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NADH binding / L-serine biosynthetic process / serine binding / NAD+ binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.75 Å | ||||||
Authors | Schuller, D.J. / Grant, G.A. / Banaszak, L.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Authors: Schuller, D.J. / Grant, G.A. / Banaszak, L.J. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Enhanced Expression of the Escherichia Coli Sera Gene in a Plasmid Vector: Purification, Crystallization, and Preliminary X-Ray Dat of D-3-Phosphoglycerate Dehydrogenase Authors: Schuller, D.J. / Fetter, C.H. / Banaszak, L.J. / Grant, G.A. #2: Journal: J.Biol.Chem. / Year: 1986 Title: The Nucleotide Sequence of the Sera Gene of Escherichia Coli and the Amino Acid Sequence of the Encoded Protein, D-3-Phosphoglycerate Dehydrogenase Authors: Tobey, K.L. / Grant, G.A. | ||||||
History |
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Remark 700 | SHEET BETA SHEET RA FROM SUBUNIT A ALIGNS WITH BETA SHEET RB OF SUBUNIT B TO FORM AN 8 STRAND SHEET. ...SHEET BETA SHEET RA FROM SUBUNIT A ALIGNS WITH BETA SHEET RB OF SUBUNIT B TO FORM AN 8 STRAND SHEET. STRAND R-4 OF ONE SUBUNIT CONTACTS STRAND R-4 OF THE OTHER. REGISTER: ASN 368 O - LEU 370 N, ASN 368 N - LEU 370 O. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1psd.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1psd.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 1psd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1psd ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1psd | HTTPS FTP |
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-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:
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Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 108 .. 294 B 109 .. 294 0.383 M2 A 7 .. 107 B 7 .. 107 0.680 M2 A 295 .. 336 B 295 .. 336 0.692 M2 A 337 .. 410 B 337 .. 410 0.622 SUBUNITS A AND B IN THIS ENTRY FORM A TETRAMER WITH SUBUNITS A' AND B' WHICH CAN BE GENERATED BY APPLYING THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATION TO THE COORDINATES IN THIS ENTRY: -1.0 0.0 0.0 136.1 0.0 -1.0 0.0 0.0 0.0 0.0 1.0 0.0 |
-Components
#1: Protein | Mass: 44095.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Strain (production host): K12 / References: UniProt: P0A9T0, phosphoglycerate dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | RESIDUES A 258, A 260, A 263 AND B 258, B 260, B 263 ARE THE GLYCINES OF GXGXXG NUCLEOTIDE BINDING ...RESIDUES A 258, A 260, A 263 AND B 258, B 260, B 263 ARE THE GLYCINES OF GXGXXG NUCLEOTIDE | Nonpolymer details | C 451, D 451 ALLOSTERIC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.72→50 Å / Num. obs: 26417 / % possible obs: 84 % |
Reflection | *PLUS Num. measured all: 287548 / Rmerge(I) obs: 0.119 |
-Processing
Software |
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Refinement | Resolution: 2.75→9 Å / σ(F): 2 Details: RESIDUES A 114 AND B 114 WERE MISTAKENLY REFINED AS ASP; BUT SHOULD BE GLU. GLU HAS BEEN SUBSTITUTED BUT NOT REFINED.
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Refinement step | Cycle: LAST / Resolution: 2.75→9 Å
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Refine LS restraints |
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