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- PDB-3odb: Haemophilus influenzae ferric binding protein A -Iron Loaded -ope... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3odb | ||||||
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Title | Haemophilus influenzae ferric binding protein A -Iron Loaded -open Conformation | ||||||
![]() | Iron-utilization periplasmic protein | ||||||
![]() | METAL BINDING PROTEIN / Periplasmic binding protein / Iron / Iron Periplasmic binding protein / FbpBC | ||||||
Function / homology | ![]() transmembrane transport / iron ion transport / outer membrane-bounded periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Khambati, H.K. / Moraes, T.F. / Singh, J. / Shouldice, S.R. / Yu, R.H. / Schryvers, A.B. | ||||||
![]() | ![]() Title: The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric binding protein A. Authors: Khambati, H.K. / Moraes, T.F. / Singh, J. / Shouldice, S.R. / Yu, R.H. / Schryvers, A.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.5 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417 KB | Display | ![]() |
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Full document | ![]() | 417.8 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kn7C ![]() 3kn8C ![]() 3od7C ![]() 1d9vS 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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Unit cell |
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Components
#1: Protein | Mass: 33769.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG 1000, 0.1 M MES, pH 6.5 , VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→106 Å / Num. all: 35614 / Num. obs: 34190 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.041 / Net I/σ(I): 60 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2437 / % possible all: 70.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1D9V Resolution: 1.62→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.953 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.819 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20
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