+Open data
-Basic information
Entry | Database: PDB / ID: 4q9w | ||||||
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Title | mTFP*: a robust and versatile host protein at 1.00 A resolution | ||||||
Components | GFP-like fluorescent chromoprotein cFP484 | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel / artificial metalloenzyme / metalloenzyme / bioconjugation / protein design / thermostable / temperature stable / solvent stable / robust | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clavularia sp. (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Fischer, J. / Quitterer, F. / Groll, M. / Eppinger, J. | ||||||
Citation | Journal: To be Published Title: mTFP*: An imperishable and versatile protein host for anchoring diverse ligands and organocatalysts 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 | 4q9w.cif.gz | 226.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q9w.ent.gz | 181.7 KB | Display | PDB format |
PDBx/mmJSON format | 4q9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q9w_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 4q9w_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 4q9w_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4q9w_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/4q9w ftp://data.pdbj.org/pub/pdb/validation_reports/q9/4q9w | HTTPS FTP |
-Related structure data
Related structure data | 4q9xC 2hqkS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25188.408 Da / Num. of mol.: 2 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, 220R, ...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, 220R, V224A, H242Y, 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-Gold(DE3) / References: UniProt: Q9U6Y3 #2: 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: 2.02 Å3/Da / Density % sol: 39.19 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1→10 Å / Num. all: 215374 / Num. obs: 204329 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1→1.1 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.8 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2HQK Resolution: 1→10 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.568 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.023 / ESU R Free: 0.024 / 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: 12.239 Å2
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Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å / Total num. of bins used: 20
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Refinement TLS params. | S32: 0.0013 Å ° / T23: -0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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