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Yorodumi- PDB-1mgv: Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mgv | ||||||
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Title | Crystal Structure of the R391A Mutant of 7,8-Diaminopelargonic Acid Synthase | ||||||
Components | 7,8-diamino-pelargonic acid aminotransferase | ||||||
Keywords | TRANSFERASE / Aminotransferase / fold type I / subclass II / homodimer | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase 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: 2.1 Å | ||||||
Authors | Eliot, A.C. / Sandmark, J. / Schneider, G. / Kirsch, J.F. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The Dual-Specific Active Site of 7,8-Diaminopelargonic Acid Synthase and the Effect of the R391A Mutation Authors: Eliot, A.C. / Sandmark, J. / Schneider, G. / Kirsch, J.F. | ||||||
History |
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Remark 999 | sequence the authors maintain that residue 14 is a leucine, as confirmed by DNA sequencing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mgv.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgv.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mgv_validation.pdf.gz | 473.7 KB | Display | wwPDB validaton report |
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Full document | 1mgv_full_validation.pdf.gz | 499.4 KB | Display | |
Data in XML | 1mgv_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1mgv_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgv ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgv | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 47224.273 Da / Num. of mol.: 2 / Mutation: R391A 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 | ChemComp-IPA / #5: 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: 2.06 Å3/Da / Density % sol: 40.43 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, MPD, HEPES, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 / 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: 1.12 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 26, 2001 |
Radiation | Monochromator: Si(111) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20.08 Å / Num. all: 44984 / Num. obs: 44984 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.168 / % possible all: 97.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 43771 / Num. measured all: 177643 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.168 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WT dimer Resolution: 2.1→20.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.417 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 32.259 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor Rfree: 0.233 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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