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Yorodumi- PDB-5dh2: Structure of the siderophore periplasmic binding protein from the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dh2 | ||||||
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Title | Structure of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca in I222 | ||||||
Components | siderophore periplasmic binding protein | ||||||
Keywords | PROTEIN BINDING / Siderophore / Periplasmic Binding Protein / fuscachelin | ||||||
Function / homology | ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / outer membrane-bounded periplasmic space / Similar to iron(III) dicitrate transport permease RBL00804 Function and homology information | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å | ||||||
Authors | Li, K. / Bruner, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2016 Title: Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca. Authors: Li, K. / Bruner, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dh2.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dh2.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dh2_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 5dh2_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 5dh2_validation.xml.gz | 20 KB | Display | |
Data in CIF | 5dh2_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/5dh2 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dh2 | HTTPS FTP |
-Related 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: 33735.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria) Strain: YX / Gene: Tfu_1864 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % / Description: rod-shaped |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.16 M ammonium acetate 32% w/v polyethylene glycol 4,000 0.1 M sodium acetate pH 4.6 PH range: 4.6-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2014 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→37.783 Å / Num. obs: 24621 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.59→37.783 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.39 / 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: 2.59→37.783 Å
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Refine LS restraints |
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LS refinement shell |
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