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Yorodumi- PDB-3waf: X-ray structure of apo-TtFbpA, a ferric ion-binding protein from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3waf | ||||||
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Title | X-ray structure of apo-TtFbpA, a ferric ion-binding protein from thermus thermophilus HB8 | ||||||
Components | Iron ABC transporter, periplasmic iron-binding protein | ||||||
Keywords | METAL BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ABC TRANSPORTER / TTHA1628 / PEAMEASES | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / ISOPROPYL ALCOHOL / Iron ABC transporter, periplasmic iron-binding protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wang, S. / Ogata, M. / Horita, S. / Ohtsuka, J. / Nagata, K. / Tanokura, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8. Authors: Wang, S. / Ogata, M. / Horita, S. / Ohtsuka, J. / Nagata, K. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3waf.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3waf.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 3waf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3waf ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3waf | HTTPS FTP |
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-Related structure data
Related structure data | 3waeC 1xvyS 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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Unit cell |
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-Components
#1: Protein | Mass: 36193.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1628 / Plasmid: pRSF vector / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q5SHV2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.77 Å3/Da / Density % sol: 30.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE (PH5.2), 20% (W/V) 2-PROPANOL, 20% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→79.29 Å / Num. obs: 47714 / Redundancy: 13.2 % |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XVY Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.072 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 24.144 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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