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Open data
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Basic information
Entry | Database: PDB / ID: 5jy9 | |||||||||
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Title | An iron-bound structure of the salicylate synthase Irp9 | |||||||||
![]() | Putative salicylate synthetase | |||||||||
![]() | ISOMERASE / chorismate / isochorismate | |||||||||
Function / homology | ![]() cellular biosynthetic process / isochorismate synthase activity / oxo-acid-lyase activity / : Similarity search - Function | |||||||||
Biological species | Yersinia enterocolitica serotype O:8 / biotype 1B | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Meneely, K.M. / Lamb, A.L. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.5 KB | Display | ![]() |
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PDB format | ![]() | 255.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jxzC ![]() 5jy4C ![]() 5jy8C ![]() 5jzdC ![]() 2fn1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48057.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 13174 / 8081 / Gene: ybtS, YE2612 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 14% PEG 8 000, 0.25 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 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: 2.16→39.12 Å / Num. obs: 47172 / % possible obs: 98.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rsym value: 0.096 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.16→2.23 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 3 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FN1 Resolution: 2.162→36.519 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 23.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.162→36.519 Å
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Refine LS restraints |
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LS refinement shell |
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