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Open data
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Basic information
Entry | Database: PDB / ID: 6om5 | ||||||
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Title | Structure of a haemophore from Haemophilus haemolyticus | ||||||
![]() | haemophore | ||||||
![]() | METAL TRANSPORT / Haemophilus haemolyticus / haemophore / antimicrobial | ||||||
Function / homology | Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / PROTOPORPHYRIN IX CONTAINING FE / Polymerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torrado, M. / Walshe, J.L. / Mackay, J.P. / Guss, J.M. / Gell, D.A. | ||||||
![]() | ![]() Title: A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae. Authors: Latham, R.D. / Torrado, M. / Atto, B. / Walshe, J.L. / Wilson, R. / Guss, J.M. / Mackay, J.P. / Tristram, S. / Gell, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.9 KB | Display | ![]() |
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Full document | ![]() | 812.1 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27400.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: M19107 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 180 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.25 % / Description: Hexagonal crystals with orange-red colour |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate, 30 mM sodium phosphate, 72 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2017 | |||||||||
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→45.52 Å / Num. obs: 62031 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Χ2: 0.97 / Net I/σ(I): 23.2 | |||||||||
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 21 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 4 / Num. unique obs: 3086 / CC1/2: 0.909 / Rpim(I) all: 0.25 / Rrim(I) all: 0.82 / Χ2: 0.86 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.667 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→41.49 Å
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Refine LS restraints |
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