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Yorodumi- PDB-1m6j: CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ENTAMOEBA HIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6j | ||||||
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Title | CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM ENTAMOEBA HISTOLYTICA | ||||||
Components | Triosephosphate Isomerase | ||||||
Keywords | ISOMERASE / Asymmetry / Entamoeba histolytica / monomer stability / triosephosphate isomerase | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Fernandez-Velasco, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structure and Inactivation of Triosephosphate Isomerase from Entamoeba histolytica Authors: Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Del Pozo-Yauner, L. / Kornhauser, A. / Fernandez-Velasco, D.A. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: Sequencing, Expression and Properties of Triosephosphate Isomerase from Entamoeba histolytica Authors: Landa, A. / Rojo-Dominguez, A. / Jimenez, A. / Fernandez-Velasco, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6j.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6j.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m6j_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 1m6j_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 1m6j_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 1m6j_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6j ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6j | HTTPS FTP |
-Related structure data
Related structure data | 5timS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27964.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): TGI / References: UniProt: O02611, triose-phosphate isomerase #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: 2.3 Å3/Da / Density % sol: 46.5 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 28% PEG 1500, 30% 1,6-hexanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K, temperature 291.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.782 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1999 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.782 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→69.75 Å / Num. all: 80900 / Num. obs: 80009 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.5→1.59 Å / % possible all: 76.1 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 80420 / % possible obs: 99.4 % / Num. measured all: 360647 / Rmerge(I) obs: 0.04 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5TIM Resolution: 1.5→69.75 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: DISCRETELY DISORDERED RESIDUES: GLN 56, THR 76, GLN 107, GLN 115, GLU 118, GLN 145, GLU 148, LYS 167, GLU 192, GLN 195, GLU 203, SER 220, LYS 251 FROM MONOMER A AND GLU 35, GLN 56, LYS 77, ...Details: DISCRETELY DISORDERED RESIDUES: GLN 56, THR 76, GLN 107, GLN 115, GLU 118, GLN 145, GLU 148, LYS 167, GLU 192, GLN 195, GLU 203, SER 220, LYS 251 FROM MONOMER A AND GLU 35, GLN 56, LYS 77, ASP 125, ARG 141, GLN 145, LYS 167, ASN 168, ILE 179, ASP 188, GLN 195, GLU 211, SER 220 FROM MONOMER B.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.7888 Å2 / ksol: 0.359535 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→69.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.184 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.278 / Rfactor Rwork: 0.253 |