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Yorodumi- PDB-4iww: Computational Design of an Unnatural Amino Acid Metalloprotein wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iww | |||||||||
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Title | Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy | |||||||||
Components | Unnatural Amino Acid Mediated Metalloprotein | |||||||||
Keywords | METAL BINDING PROTEIN / computational design / TIM barrel / metalloprotein / bipyridylalanine | |||||||||
Function / homology | Function and homology information indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Mills, J. / Bolduc, J. / Khare, S. / Stoddard, B. / Baker, D. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy. Authors: Mills, J.H. / Khare, S.D. / Bolduc, J.M. / Forouhar, F. / Mulligan, V.K. / Lew, S. / Seetharaman, J. / Tong, L. / Stoddard, B.L. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iww.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iww.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 4iww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iww_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 4iww_full_validation.pdf.gz | 473.3 KB | Display | |
Data in XML | 4iww_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4iww_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/4iww ftp://data.pdbj.org/pub/pdb/validation_reports/iw/4iww | HTTPS FTP |
-Related structure data
Related structure data | 4ix0C 4j9tC 1igsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 248 / Label seq-ID: 1 - 247
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-Components
#1: Protein | Mass: 29774.086 Da / Num. of mol.: 2 Mutation: K10E, F22V, S70A, K110M, I133BPA, N161T, N179T, R181Q, L183D, E209D, F246L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trpC, SSO0895 / Plasmid: pet28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06121 #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: 1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 26, 2012 / Details: Varimax HR |
Radiation | Monochromator: Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→123.6 Å / Num. all: 22369 / Num. obs: 20826 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 20.86 Å2 / Rsym value: 0.041 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.3 % / Num. unique all: 2195 / Rsym value: 0.079 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IGS Resolution: 2.3→123.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.033 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.555 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 19.841 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→123.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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