+Open data
-Basic information
Entry | Database: PDB / ID: 6lb8 | ||||||
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Title | Crystal structure of the Ca2+-free T4L-MICU1-MICU2 complex | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Calcium binding protein / Mitochondrial / Uniporter / EF-hand | ||||||
Function / homology | Function and homology information negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import ...negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import / viral release from host cell by cytolysis / Mitochondrial protein degradation / calcium channel complex / peptidoglycan catabolic process / mitochondrial membrane / protein homooligomerization / mitochondrial intermembrane space / defense response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / mitochondrial inner membrane / defense response to bacterium / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia virus T4 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.283 Å | ||||||
Authors | Wu, W. / Shen, Q. / Zheng, J. / Jia, Z. | ||||||
Funding support | China, 1items
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Citation | |||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lb8.cif.gz | 326.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lb8.ent.gz | 258.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lb8_validation.pdf.gz | 476.5 KB | Display | wwPDB validaton report |
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Full document | 6lb8_full_validation.pdf.gz | 520.6 KB | Display | |
Data in XML | 6lb8_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 6lb8_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/6lb8 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/6lb8 | HTTPS FTP |
-Related structure data
Related structure data | 6lb7C 4nscS 6iihS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60321.707 Da / Num. of mol.: 2 / Mutation: C54T,C97A Source method: isolated from a genetically manipulated source Details: The fusion protein of T4L Endolysin, Linker, and Calcium uptake protein 1 Source: (gene. exp.) Escherichia virus T4, (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, MICU1, CALC, CBARA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D9IEF7, UniProt: Q9BPX6, lysozyme #2: Protein | Mass: 38719.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IYU8 |
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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: 2.38 Å3/Da / Density % sol: 48.24 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2% tacsimate pH 5.0, 0.1 M sodium citrate pH 5.0, 12% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 3.283→49.06 Å / Num. obs: 29560 / % possible obs: 99 % / Redundancy: 13 % / CC1/2: 0.958 / Rmerge(I) obs: 0.1947 / Rrim(I) all: 0.2028 / Net I/σ(I): 15.12 |
Reflection shell | Resolution: 3.283→3.401 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.505 / Num. unique obs: 2680 / CC1/2: 0.937 / Rrim(I) all: 0.5255 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NSC, 6IIH Resolution: 3.283→49.056 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.61 Å2 / Biso mean: 39.8777 Å2 / Biso min: 4.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.283→49.056 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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