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Yorodumi- PDB-1d2f: X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d2f | ||||||
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Title | X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION | ||||||
Components | MALY PROTEIN | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE FOLD / LARGE PLP-BINDING DOMAIN / SMALL C-TERMINAL DOMAIN / OPEN ALPHA-BETA STRUCTURE. | ||||||
Function / homology | Function and homology information cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / L-cysteine desulfhydrase activity / methionine biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Clausen, T. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression. Authors: Clausen, T. / Schlegel, A. / Peist, R. / Schneider, E. / Steegborn, C. / Chang, Y.S. / Haase, A. / Bourenkov, G.P. / Bartunik, H.D. / Boos, W. #1: Journal: J.Bacteriol. / Year: 1995 Title: Maly of Escherichia-Coli Is an Enzyme With the Activity of a Beta-C-S Lyase (Cystathionase). Authors: Zdych, E. / Peist, R. / Reidl, J. / Boos, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d2f.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d2f.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 1d2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d2f_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 1d2f_full_validation.pdf.gz | 480.7 KB | Display | |
Data in XML | 1d2f_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 1d2f_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/1d2f ftp://data.pdbj.org/pub/pdb/validation_reports/d2/1d2f | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43684.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PJR115 / Production host: Escherichia coli (E. coli) / References: UniProt: P23256 #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: 2.26 Å3/Da / Density % sol: 45.58 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: AMMONIUM SULPHATE, MES, TRIS, DITHITHREITOL, pH 7.0, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 4, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 94388 / Num. obs: 24839 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.303 / % possible all: 88.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 94388 |
Reflection shell | *PLUS % possible obs: 88.7 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER / Details: ENERGY RESTRAINED CRYSTALLOGRAPHIC REFINEMENT.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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