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Yorodumi- PDB-1mly: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mly | ||||||
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Title | Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin | ||||||
Components | 7,8-diamino-pelargonic acid aminotransferase | ||||||
Keywords | TRANSFERASE / Aminotransferase / Fold type I / subclass II / amiclenomycin | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Sandmark, J. / Mann, S. / Marquet, A. / Schneider, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin Authors: Sandmark, J. / Mann, S. / Marquet, A. / Schneider, G. | ||||||
History |
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Remark 999 | sequence The crystallized protein differs from the Swissprot sequence at residue 14. In the ...sequence The crystallized protein differs from the Swissprot sequence at residue 14. In the Swissprot sequence number 14 is a tryptophan while here it is a leucin. This is confirmed by DNA sequencing and was also reported for the original WT structure (1qj5). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mly.cif.gz | 191.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mly.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mly_validation.pdf.gz | 474 KB | Display | wwPDB validaton report |
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Full document | 1mly_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | 1mly_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1mly_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1mly ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1mly | HTTPS FTP |
-Related 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: 47310.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioA / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | In both subunits the cofactor pyridoxal-5'-phosphate forms a covalent adduct with the inhibitor ...In both subunits the cofactor pyridoxal-5'-phosphate forms a covalent adduct with the inhibitor amiclenomycin, followed by aromatization of amiclenomycin hexadiene ring. The binding mode for the inhibitor is different in the two subunits. The electron density for the covalent adduct between amiclenomycin and pyridoxal-5'-phosphate is better in monomer A. For details see the primary citation. | |
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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: 2.08 Å3/Da / Density % sol: 40.91 % | ||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Kack, H., (1998) Acta Crystallogr., D54, 1397. | ||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.968 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 16, 2001 |
Radiation | Monochromator: Si(111) monocromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→40.16 Å / Num. all: 70391 / Num. obs: 70391 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.81→1.91 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.259 / % possible all: 94.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 69507 / Num. measured all: 276229 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Lowest resolution: 1.9 Å / % possible obs: 94.1 % / Rmerge(I) obs: 0.259 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.533 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: In monomer A two stretches of residues are disordered, 159-168 and 180-189 resp. In monomer B three stretches of residues are disordered, 159-168, 180-189 and 299-303 resp. Residue 429 was ...Details: In monomer A two stretches of residues are disordered, 159-168 and 180-189 resp. In monomer B three stretches of residues are disordered, 159-168, 180-189 and 299-303 resp. Residue 429 was excluded from both monomers. A number of side chains on the surface of the protein are disordered. The occupancy for these is estimated to 0 in most cases. In four cases the side chains are given the occupancy 0.5.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.858 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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