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Open data
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Basic information
Entry | Database: PDB / ID: 6eu8 | |||||||||
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Title | Crystal structure of Tannerella forsythia Apo HmuY analog (TFO) | |||||||||
![]() | Putative heme binding protein | |||||||||
![]() | heme-binding protein | |||||||||
Function / homology | HmuY protein / HmuY protein / MALONATE ION / Putative heme binding protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Antonyuk, S.V. / Strange, R.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Tannerella forsythiaTfo belongs toPorphyromonas gingivalisHmuY-like family of proteins but differs in heme-binding properties. Authors: Bielecki, M. / Antonyuk, S. / Strange, R.W. / Smalley, J.W. / Mackiewicz, P. / Smiga, M. / Stepien, P. / Olczak, M. / Olczak, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 433.9 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ewmC ![]() 3uu2S S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 22415.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MLI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Sodium malonate, Tris pH 7.5 / Temp details: room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016 |
Radiation | Monochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92818 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→49.34 Å / Num. obs: 41705 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.011 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 9 % / Rmerge(I) obs: 2.1 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2033 / CC1/2: 0.6 / Rpim(I) all: 0.76 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UU2 Resolution: 1.47→49.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.577 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.07 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.101 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→49.34 Å
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Refine LS restraints |
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