+Open data
-Basic information
Entry | Database: PDB / ID: 1d9v | ||||||
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Title | HAEMOPHILUS INFLUENZAE FERRIC-BINDING PROTEIN APO FORM | ||||||
Components | PROTEIN (iron-utilization periplasmic protein) | ||||||
Keywords | METAL BINDING PROTEIN / FERRIC / BINDING PROTEIN / IRON / APO FORM / PERIPLASMIC PROTEIN / ABC CASSETTE RECEPTOR PROTEIN | ||||||
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 / Resolution: 1.75 Å | ||||||
Authors | McRee, D.E. / Bruns, C.M. / Williams, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+-binding protein. Authors: Bruns, C.M. / Anderson, D.S. / Vaughan, K.G. / Williams, P.A. / Nowalk, A.J. / McRee, D.E. / Mietzner, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d9v.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9v.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9v ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9v | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 33769.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Description: GRAM-NEGATIVE HUMAN PATHOGENIC BACTERIA / Gene: HITA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35755 |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.09 Å3/Da / Density % sol: 41.23 % | ||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 1450, HEPES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. all: 27731 / Num. obs: 27731 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.75→1.86 Å / Rmerge(I) obs: 0.37 / Num. unique all: 3703 / % possible all: 77 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 27754 / Redundancy: 6.7 % |
Reflection shell | *PLUS % possible obs: 77 % / Redundancy: 3.5 % / Num. unique obs: 3703 |
-Processing
Software |
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Refinement | Resolution: 1.75→100 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.75→100 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Rfactor obs: 0.179 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.22 | |||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.86 Å / Rfactor Rfree: 0.38 / Rfactor obs: 0.37 |