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Yorodumi- PDB-2qb0: Structure of the 2TEL crystallization module fused to T4 lysozyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qb0 | ||||||
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Title | Structure of the 2TEL crystallization module fused to T4 lysozyme with an Ala-Gly-Pro linker. | ||||||
Components |
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Keywords | HYDROLASE REGULATOR / Helical polymer | ||||||
Function / homology | Function and homology information Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / viral release from host cell by cytolysis / Signaling by FLT3 fusion proteins / peptidoglycan catabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / viral release from host cell by cytolysis / Signaling by FLT3 fusion proteins / peptidoglycan catabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / DNA-binding transcription activator activity, RNA polymerase II-specific / host cell cytoplasm / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Nauli, S. / Bowie, J.U. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Polymer-driven crystallization. Authors: Nauli, S. / Farr, S. / Lee, Y.J. / Kim, H.Y. / Faham, S. / Bowie, J.U. | ||||||
History |
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Remark 999 | SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE TELSAM DOMAINS IN CHAINS A, ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE TELSAM DOMAINS IN CHAINS A, B, C AND D AT THE TIME OF PROCESSING THIS ENTRY. THE RESIDUE ALA, GLY, PRO FORM A LINKER IN THE CHIMERIC PROTEIN IN CHAINS B AND D |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qb0.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qb0.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qb0_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 2qb0_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 2qb0_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 2qb0_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/2qb0 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/2qb0 | HTTPS FTP |
-Related structure data
Related structure data | 2qarC 2qb1C 1ji7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Details | This assembly is not biological. A helical hexamer is formed by applying the P32 symmetry on the asymmetric unit. The SAM moiety (the first 160 residues or so) have been shown numerous times in the literature to form a helical polymer. |
-Components
#1: Protein | Mass: 9252.510 Da / Num. of mol.: 2 / Mutation: E80V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P41212 #2: Protein | Mass: 27720.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P00720, lysozyme #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | |
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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: 3.15 Å3/Da / Density % sol: 60.9 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→90 Å / Num. obs: 29148 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.062 / Χ2: 1.001 / Net I/σ(I): 17.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JI7 Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.235 / SU B: 16.28 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.519 / ESU R Free: 0.289 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.141 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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