[English] 日本語
Yorodumi- PDB-1dkw: CRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED SUB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dkw | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF TRIOSE-PHOSPHATE ISOMERASE WITH MODIFIED SUBSTRATE BINDING SITE | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / TIM BARREL / MODIFIED LOOP-8 | ||||||
Function / homology | Function and homology information glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.65 Å | ||||||
Authors | Norledge, B.V. / Lambeir, A.M. / Abagyan, R.A. / Rottman, A. / Fernandez, A.M. / Filimonov, V.V. / Peter, M.G. / Wierenga, R.K. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity. Authors: Norledge, B.V. / Lambeir, A.M. / Abagyan, R.A. / Rottmann, A. / Fernandez, A.M. / Filimonov, V.V. / Peter, M.G. / Wierenga, R.K. #1: 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. / Radha Kishan, K.V. / Zeelen, J.P. / Wierenga, R.K. #2: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dkw.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dkw.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkw ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkw | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25787.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Production host: Escherichia coli (E. coli) / References: UniProt: P04789, triose-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0 M CITRIC ACID PH 6.5, 20% PEG6000, 2.5% T-BUTANOL, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→22 Å / Num. all: 12311 / Num. obs: 12311 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.181 / % possible all: 73.4 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 22 Å / Num. obs: 13258 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Biso Wilson estimate: 40 Å2 |
Reflection shell | *PLUS Highest resolution: 2.65 Å / Lowest resolution: 2.74 Å / % possible obs: 73.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.65→22 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→22 Å
| |||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.65 Å / Lowest resolution: 22 Å / Num. reflection all: 12114 / Num. reflection obs: 12114 / σ(I): 0 / σ(F): 0 / Num. reflection Rfree: 593 / % reflection Rfree: 5 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.183 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.013 |