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Yorodumi- PDB-4r6d: Modified mTFP* for enhanced metal binding: co-crystallization wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r6d | ||||||
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Title | Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2 | ||||||
Components | GFP-like fluorescent chromoprotein cFP484 | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel topology / engineered metalloenzyme / Diels-Alderase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clavularia sp. (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2 Authors: Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r6d.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r6d.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r6d_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 4r6d_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 4r6d_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4r6d_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6d ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6d | HTTPS FTP |
-Related structure data
Related structure data | 4q9wS S: Starting model for refinement |
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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
#1: Protein | Mass: 24825.068 Da / Num. of mol.: 1 / Fragment: unp residues 44-258 Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, ...Mutation: H63Y, H80N, L82I, S100T, N101T, Q104A, L110F, A118P, D119N, M151L, R161Y, F162L, D163K, M165E, L179T, K180G, E182D, P183A, I187R, V196K, I199V, S200K, S202K, H210Y, C213V, S217T, K220R, V224A, I239C, Y246H, L251V, N254S, Y259N, L261T, L262F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clavularia sp. (invertebrata) / Plasmid: pET303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q9U6Y3 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25.9% PEG3000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2014 |
Radiation | Monochromator: BRUKER MICROSTAR MICRO-FOCUS (MONTEL OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70 Å / Num. all: 32546 / Num. obs: 32526 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.55→1.65 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4Q9W Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.44 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.08 / 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: 14.456 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.589 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.9045 Å / Origin y: -2.5472 Å / Origin z: -3.564 Å
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Refinement TLS group |
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