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Yorodumi- PDB-1iov: COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iov | ||||||
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Title | COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE | ||||||
Components | D-ALA\:D-ALA LIGASE | ||||||
Keywords | LIGASE / GLYCOGEN PHOSPHORYLASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS / VANCOMYCIN / ADP BINDING | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / protein homodimerization activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Knox, J.R. / Moews, P.C. / Fan, C. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Authors: Fan, C. / Park, I.S. / Walsh, C.T. / Knox, J.R. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: A Common Fold for Peptide Synthetases Cleaving ATP to Adp Authors: Fan, C. / Moews, P.C. / Shi, Y. / Walsh, C.T. / Knox, J.R. #2: Journal: Science / Year: 1994 Title: Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 A Resolution Authors: Fan, C. / Moews, P.C. / Walsh, C.T. / Knox, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iov.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iov.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1iov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1iov ftp://data.pdbj.org/pub/pdb/validation_reports/io/1iov | HTTPS FTP |
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-Related structure data
Related structure data | 1iowC 2dlnS S: Starting model for refinement C: citing same article (ref.) |
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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: 32867.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: ENZYME PROVIDED BY C.T. WALSH, HARVARD MED SCHOOL. SEE ZAWADZKE ET AL. BIOCHEM. 30, P. 1673, 1991. Gene (production host): DDLB / Production host: Escherichia coli (E. coli) / References: UniProt: P07862, D-alanine-D-alanine ligase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-POB / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.17 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: AMMONIUM SULFATE, pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 11579 / % possible obs: 75 % / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.1→2.4 Å / % possible all: 39 |
Reflection | *PLUS Num. obs: 10991 / Num. measured all: 34347 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.45 Å / % possible obs: 55 % / Num. unique obs: 3959 / Num. measured obs: 8020 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DLN Resolution: 2.2→15 Å / σ(F): 3
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Displacement parameters | Biso mean: 10.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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