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- PDB-7qxv: Crystal Structure of Haem-Binding Protein HemS Mutant F104A F199A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qxv | ||||||
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Title | Crystal Structure of Haem-Binding Protein HemS Mutant F104A F199A, from Yersinia enterocolitica | ||||||
![]() | Hemin transport protein | ||||||
![]() | METAL BINDING PROTEIN / iron / haem-degrading enzyme / host-pathogen interactions | ||||||
Function / homology | Haemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / iron ion transport / DI(HYDROXYETHYL)ETHER / Hemin transport protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Barker, P.D. / Keith, A. / Brear, P. / Wales, D. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal Structure of Haem-Binding Protein HemS Mutant F104A F199A, from Yersinia enterocolitica Authors: Barker, P.D. / Keith, A. / Brear, P. / Wales, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j0pS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 39107.699 Da / Num. of mol.: 1 / Mutation: F104A F199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM tris-HCl 1.8 M (NH4)2SO4, 2% (w/v) PEG 400 / PH range: 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 1, 2021 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.67→50.57 Å / Num. obs: 37692 / % possible obs: 100 % / Redundancy: 18.6 % / Rpim(I) all: 0.096 / Rrim(I) all: 0.415 / Net I/σ(I): 5.6 / Num. measured all: 701834 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2J0P Resolution: 1.67→50.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 13.711 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.68 Å2 / Biso mean: 50.554 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 1.67→50.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.671→1.714 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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