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Yorodumi- PDB-4pcf: Structure-based protein engineering of a monomeric triosephosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pcf | ||||||||||||
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Title | Structure-based protein engineering of a monomeric triosephosphate isomerase towards changing substrate specificity | ||||||||||||
Components | Ma18-TIM | ||||||||||||
Keywords | ISOMERASE / TRIOSEPHOSPHATE ISOMERASE / TIM BARREL / PROTEIN ENGINEERING / SUBSTRATE SPECIFICITY | ||||||||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.71 Å | ||||||||||||
Authors | Krause, M. / Neubauer, P. / Wierenga, R.K. | ||||||||||||
Funding support | Finland, Germany, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structures of two monomeric triosephosphate isomerase variants identified via a directed-evolution protocol selecting for L-arabinose isomerase activity. Authors: Krause, M. / Kiema, T.R. / Neubauer, P. / Wierenga, R.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pcf.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pcf.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 4pcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pcf_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 4pcf_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 4pcf_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4pcf_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/4pcf ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pcf | HTTPS FTP |
-Related 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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 25836.600 Da / Num. of mol.: 3 / Mutation: E23G, A70T, S96F, A178V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Plasmid: pMK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P04789*PLUS, triose-phosphate isomerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.75M (NH4)2HPO4, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→83.94 Å / Num. obs: 19927 / % possible obs: 99.5 % / Redundancy: 6.96 % / Net I/σ(I): 12.46 |
Reflection shell | Resolution: 2.71→2.73 Å / Redundancy: 1.23 % / Mean I/σ(I) obs: 2.49 / % possible all: 56.3 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.71→83.94 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.798 / SU B: 18.335 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / 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: 17.806 Å2
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Refinement step | Cycle: 1 / Resolution: 2.71→83.94 Å
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Refine LS restraints |
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