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Yorodumi- PDB-1nnf: Crystal Structure Analysis of Haemophlius Influenzae Ferric-ion B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nnf | ||||||
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Title | Crystal Structure Analysis of Haemophlius Influenzae Ferric-ion Binding Protein H9Q Mutant Form | ||||||
Components | Iron-utilization periplasmic protein | ||||||
Keywords | METAL BINDING PROTEIN / IRON-BINDING PROTEIN / EDTA-FE-PROTEIN COMPLEX | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Shouldice, S.R. / Dougan, D.R. / Skene, R.J. / Tari, L.W. / McRee, D.E. / Yu, R.-H. / Schryvers, A.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: High Resolution Structure of an Alternate Form of the Ferric ion Binding Protein from Haemophilus influenzae Authors: Shouldice, S.R. / Dougan, D.R. / Skene, R.J. / Tari, L.W. / McRee, D.E. / 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 | 1nnf.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nnf.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/1nnf ftp://data.pdbj.org/pub/pdb/validation_reports/nn/1nnf | HTTPS FTP |
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-Related structure data
Related structure data | 1d9vS 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: 33759.230 Da / Num. of mol.: 1 / Mutation: H9Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: 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-EDT / {[-( |
#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: 1.74 Å3/Da / Density % sol: 28.77 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: PEG 5000, Tris HCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→105.41 Å / Num. obs: 89423 |
Reflection shell | Resolution: 1.1→1.14 Å / Rsym value: 0.199 / % possible all: 36.1 |
Reflection | *PLUS % possible obs: 86.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 36.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D9V Resolution: 1.1→105.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.428 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.038 / ESU R Free: 0.037 / 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 mean: 9.042 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→105.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.127 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor Rwork: 0.1582 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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