+Open data
-Basic information
Entry | Database: PDB / ID: 1y2f | ||||||
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Title | Crystal Structure of ZipA with an inhibitor | ||||||
Components | Cell division protein zipA | ||||||
Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information divisome complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mosyak, L. / Rush, T.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction Authors: Rush, T.S. / Grant, J.A. / Mosyak, L. / Nicholls, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y2f.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y2f.ent.gz | 32.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/1y2f ftp://data.pdbj.org/pub/pdb/validation_reports/y2/1y2f | HTTPS FTP |
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-Related structure data
Related structure data | 1y2gC 1f46S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 15533.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P77173 |
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#2: Chemical | ChemComp-WAI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, temperature 298.0K, pH 6.00 |
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 13540 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F46 Resolution: 2→43.41 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 87093.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→43.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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