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- PDB-2why: Crystal structure of the triscatecholate siderophore binding prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2why | ||||||||||||
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Title | Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Bacillibactin | ||||||||||||
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![]() | TRANSPORT PROTEIN / BACILLIBACTIN AND ENTEROBACTIN BINDING / TRISCATECHOLATE BINDING PROTEIN / IRON TRANSPORT / HIGH AFFINITY IRON IMPORT / IRON / MEMBRANE / PALMITATE / TRANSPORT / ABC-TYPE TRANSPORTER BINDING PROTEIN / SIDEROPHORE BINDING PROTEIN / LIPOPROTEIN / CELL MEMBRANE / ION TRANSPORT | ||||||||||||
Function / homology | ![]() iron ion transport / outer membrane-bounded periplasmic space / membrane raft / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Peuckert, F. / Miethke, M. / Albrecht, A.G. / Essen, L.-O. / Marahiel, M.A. | ||||||||||||
![]() | ![]() Title: Structural Basis and Stereochemistry of Triscatecholate Siderophore Binding by Feua. Authors: Peuckert, F. / Miethke, M. / Albrecht, A.G. / Essen, L.-O. / Marahiel, M.A. | ||||||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 440.7 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wi8C ![]() 2phzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34746.660 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 900.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-FE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.74 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.2; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYO PROTECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 24, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.76 Å / Num. obs: 28022 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.416 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PHZ Resolution: 1.7→19.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.9 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.51 Å
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Refine LS restraints |
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