+Open data
-Basic information
Entry | Database: PDB / ID: 6txn | ||||||
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Title | Crystal structure of thermotoga maritima Ferritin in apo form | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Metal binding / engineered protein | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Wilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Nanoscale / Year: 2021 Title: A single residue can modulate nanocage assembly in salt dependent ferritin. Authors: Kumar, M. / Markiewicz-Mizera, J. / Janna Olmos, J.D. / Wilk, P. / Grudnik, P. / Biela, A.P. / Jemiola-Rzeminska, M. / Gorecki, A. / Chakraborti, S. / Heddle, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6txn.cif.gz | 525.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6txn.ent.gz | 444.5 KB | Display | PDB format |
PDBx/mmJSON format | 6txn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6txn_validation.pdf.gz | 9.2 MB | Display | wwPDB validaton report |
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Full document | 6txn_full_validation.pdf.gz | 9.2 MB | Display | |
Data in XML | 6txn_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 6txn_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/6txn ftp://data.pdbj.org/pub/pdb/validation_reports/tx/6txn | HTTPS FTP |
-Related structure data
Related structure data | 6txhC 6txiC 6txjC 6txkC 6txlC 6txmC 1vlgS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 19401.840 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin |
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-Non-polymers , 5 types, 677 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-LFA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2 M MgCl2, 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0. 1ul of 10mg/mL protein was mixed with same amount of well solution, crystals normally appears in 2 days |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978631 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Monochromator: 0.978631 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978631 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→49.22 Å / Num. obs: 140330 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.01→7.78 Å / Rmerge(I) obs: 1.526 / Num. unique obs: 13704 / CC1/2: 0.395 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vlg Resolution: 2.01→48.276 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 343.19 Å2 / Biso mean: 57.4759 Å2 / Biso min: 27.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→48.276 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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