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Yorodumi- PDB-1p7t: Structure of Escherichia coli malate synthase G:pyruvate:acetyl-C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p7t | |||||||||
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Title | Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution | |||||||||
Components | (Malate synthase ...) x 2 | |||||||||
Keywords | LYASE / TIM barrel / Glyoxylate cycle / Acetyl-COA / cysteine-sulfenic acid | |||||||||
Function / homology | Function and homology information malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli str. K12 substr. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Anstrom, D.M. / Kallio, K. / Remington, S.J. | |||||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Structure of the Escherichia Coli Malate Synthase G:pyruvate:acetyl-coenzyme A Abortive Ternary Complex at 1.95 Angstrom Resolution Authors: Anstrom, D.M. / Kallio, K. / Remington, S.J. | |||||||||
History |
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Remark 999 | Initiating Methionine |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p7t.cif.gz | 301.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p7t.ent.gz | 237.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/1p7t ftp://data.pdbj.org/pub/pdb/validation_reports/p7/1p7t | HTTPS FTP |
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-Related structure data
Related structure data | 1d8cS 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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-Components
-Malate synthase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 81652.516 Da / Num. of mol.: 1 / Mutation: S2A, C-terminal LEHHHHHH tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria) Species: Escherichia coli / Strain: W3110 / Gene: GLCB OR GLC OR B2976 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109(DE3) / References: UniProt: P37330, malate synthase |
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#2: Protein | Mass: 81668.516 Da / Num. of mol.: 1 / Mutation: S2A, C-terminal LEHHHHHH tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria) Species: Escherichia coli / Strain: W3110 / Gene: GLCB OR GLC OR B2976 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109(DE3) / References: UniProt: P37330, malate synthase |
-Non-polymers , 6 types, 592 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: 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: 2.53 Å3/Da / Density % sol: 50.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.9 Details: MgCl2, Tris, DTT, pyruvate, acetyl-Coenzyme A, HEPES, PEG-8000, sodium acetate, pH 7.9, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.008 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→39.22 Å / Num. all: 108075 / Num. obs: 107535 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→2.06 Å / % possible all: 90.3 |
Reflection | *PLUS Num. obs: 108075 / Redundancy: 3.3 % / Num. measured all: 591192 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 90.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D8C Resolution: 1.95→39.22 Å / Isotropic thermal model: TNT correlated B'S / σ(F): 0 / Stereochemistry target values: TNT Geometry Library
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Refinement step | Cycle: LAST / Resolution: 1.95→39.22 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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