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Yorodumi- PDB-3kn7: Crystal Structure of Haemophilus influenzae Y195A mutant Holo Fer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kn7 | ||||||
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Title | Crystal Structure of Haemophilus influenzae Y195A mutant Holo Ferric ion-Binding Protein A | ||||||
Components | Iron-utilization periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / iron binding protein / Ion transport / Iron / Iron transport / Metal-binding / Transport | ||||||
Function / homology | Function and homology information transmembrane transport / iron ion transport / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å | ||||||
Authors | Shouldice, S.R. / Schryvers, A.B. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kn7.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kn7.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3kn7 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3kn7 | HTTPS FTP |
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-Related structure data
Related structure data | 3kn8C 3od7C 3odbC 1d9vS 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: 33677.156 Da / Num. of mol.: 1 / Mutation: Y195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: fbp, fbpA, HI0097, hitA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: P35755 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 34% PEG 550 MME, 0.1 M Tris pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jul 6, 2002 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→62 Å / Num. all: 31286 / Num. obs: 30268 / % possible obs: 96.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.53 % / Biso Wilson estimate: 16.071 Å2 / Rsym value: 0.0437 / Net I/σ(I): 15.16 |
Reflection shell | Resolution: 1.7→1.78 Å / Mean I/σ(I) obs: 6.67 / Rsym value: 0.0694 / % possible all: 96.75 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D9V Resolution: 1.71→62 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 2.105 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.126 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.46 Å2 / Biso mean: 17.37 Å2 / Biso min: 7.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.713→1.758 Å / Total num. of bins used: 20
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