+Open data
-Basic information
Entry | Database: PDB / ID: 5jy8 | ||||||||||||
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Title | An iron-bound structure of the isochorismate synthase EntC | ||||||||||||
Components | Isochorismate synthase EntC | ||||||||||||
Keywords | ISOMERASE | ||||||||||||
Function / homology | Function and homology information isochorismate synthase / isochorismate synthase activity / salicylic acid biosynthetic process / enterobactin biosynthetic process / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.942 Å | ||||||||||||
Authors | Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Lamb, A.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: An Open and Shut Case: The Interaction of Magnesium with MST Enzymes. Authors: Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Moran, G.R. / Lamb, A.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jy8.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jy8.ent.gz | 221.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jy8_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 5jy8_full_validation.pdf.gz | 467.3 KB | Display | |
Data in XML | 5jy8_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 5jy8_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/5jy8 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/5jy8 | HTTPS FTP |
-Related structure data
Related structure data | 5jxzC 5jy4C 5jy9C 5jzdC 3hwoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42976.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: entC, Z0735, ECs0632 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEJ3, isochorismate synthase #2: Chemical | ChemComp-FE / #3: Chemical | |
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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: 2.53 Å3/Da / Density % sol: 51.31 % |
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Crystal grow | Temperature: 298.15 K / Method: microbatch / pH: 6 Details: 0.1 M MES pH 6.0, 60% PEG 200, 0.05 M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.739 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2015 / Details: Mirror: Rh coated flat mirror |
Radiation | Monochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.739 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→38.86 Å / Num. obs: 19603 / % possible obs: 99.4 % / Redundancy: 27.6 % / CC1/2: 0.998 / Rsym value: 0.167 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 5.6 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HWO Resolution: 2.942→38.861 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.942→38.861 Å
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Refine LS restraints |
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LS refinement shell |
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