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Yorodumi- PDB-2xuz: Crystal structure of the triscatecholate siderophore binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xuz | ||||||
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Title | Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Enterobactin | ||||||
Components | IRON-UPTAKE SYSTEM-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / HIGH AFFINITY IRON IMPORT / BACILLIBACTIN AND ENTEROBACTIN BINDING / IRON TRANSPORT | ||||||
Function / homology | Function and homology information iron ion transport / outer membrane-bounded periplasmic space / membrane raft / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Peuckert, F. / Miethke, M. / Schwoerer, C.J. / Albrecht, A.G. / Oberthuer, M. / Marahiel, M.A. | ||||||
Citation | Journal: Chem.Biol. / Year: 2011 Title: The Siderophore Binding Protein Feua Shows Limited Promiscuity Toward Exogenous Triscatecholates Authors: Peuckert, F. / Ramos-Vega, A.L. / Miethke, M. / Schwoerer, C.J. / Albrecht, A.G. / Oberthuer, M. / Marahiel, M.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xuz.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xuz.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xuz_validation.pdf.gz | 974 KB | Display | wwPDB validaton report |
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Full document | 2xuz_full_validation.pdf.gz | 975.5 KB | Display | |
Data in XML | 2xuz_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2xuz_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/2xuz ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xuz | HTTPS FTP |
-Related structure data
Related structure data | 2xv1C 2whyS 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
-Protein , 1 types, 1 molecules A
#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.) BACILLUS SUBTILIS (bacteria) / Strain: ATCC 21332 / Plasmid: POK01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40409 |
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-Non-polymers , 6 types, 154 molecules
#2: Chemical | ChemComp-EB4 / | ||||
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#3: Chemical | ChemComp-FE / | ||||
#4: Chemical | ChemComp-PG4 / | ||||
#5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE TWO DIFFERRENCES BETWEEN THE COORDINATE FILE AND AND THE UNIPROT SEQUENCE (T161 AND I218) ARE ...THE TWO DIFFERRENC |
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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: 1.86 Å3/Da / Density % sol: 33.74 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: PROTEIN WAS CRYSTALLIZED FROM 34% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2010 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.83 Å / Num. obs: 19907 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.445 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WHY Resolution: 1.9→41.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.139 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.175 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.421 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.83 Å
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Refine LS restraints |
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