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Yorodumi- PDB-1ml1: PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ml1 | ||||||
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Title | PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OF A SEVEN RESIDUE LOOP | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / COMPLEX (ISOMERASE-PHOSPHOGLYCOLIC ACID) / INTRAMOLECULAR OXIDOREDUCTASE / LOOP DESIGN | ||||||
Function / homology | Function and homology information glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Thanki, N. / Zeelen, J.P. / Mathieu, M. / Jaenicke, R. / Abagyan, R.A. / Wierenga, R. / Schliebs, W. | ||||||
Citation | Journal: Protein Eng. / Year: 1997 Title: Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. Authors: Thanki, N. / Zeelen, J.P. / Mathieu, M. / Jaenicke, R. / Abagyan, R.A. / Wierenga, R.K. / Schliebs, W. #1: Journal: Protein Sci. / Year: 1996 Title: Active Site Properties of Monomeric Triosephosphate Isomerase (Monotim) as Deduced from Mutational and Structural Studies Authors: Schliebs, W. / Thanki, N. / Eritja, R. / Wierenga, R. #2: Journal: Structure / Year: 1995 Title: Three New Crystal Structures of Point Mutation Variants of Monotim: Conformational Flexibility of Loop-1, Loop-4 and Loop-8 Authors: Borchert, T.V. / Kishan, K.V. / Zeelen, J.P. / Schliebs, W. / Thanki, N. / Abagyan, R. / Jaenicke, R. / Wierenga, R.K. #3: Journal: Structure / Year: 1993 Title: The Crystal Structure of an Engineered Monomeric Triosephosphate Isomerase, Monotim: The Correct Modelling of an Eight-Residue Loop Authors: Borchert, T.V. / Abagyan, R. / Kishan, K.V.R. / Zeelen, J.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 | 1ml1.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ml1.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ml1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1ml1 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1ml1 | HTTPS FTP |
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-Related structure data
Related structure data | 1ttjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 26136.889 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Cell line: XL1-BLUE / Plasmid: BL21 / Species (production host): Escherichia coli / Cell line (production host): XL1-BLUE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | ChemComp-PGA / #3: 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: 2.6 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: PLEASE SEE JRNL ARTICLE, pH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→21 Å / Num. obs: 45363 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3 / % possible all: 96.2 |
Reflection | *PLUS Num. measured all: 124266 |
Reflection shell | *PLUS % possible obs: 96.2 % / Rmerge(I) obs: 0.297 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTJ Resolution: 2.6→32 Å / Rfactor Rfree error: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→32 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |