[English] 日本語
Yorodumi- PDB-4ymz: DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ymz | ||||||
---|---|---|---|---|---|---|---|
Title | DHAP bound Leptospira Interrogans Triosephosphate Isomerase (LiTIM) | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM BARRELS / BETA-ALPHA BARRELS / DIHYDROXYACETONE PHOSPHATE / GLYCOLYSIS | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Leptospira interrogans serovar Icterohaemorrhagiae str. RGA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Pareek, V. / Balaram, P. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Chembiochem / Year: 2016 Title: Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme Authors: Pareek, V. / Samanta, M. / Joshi, N.V. / Balaram, H. / Murthy, M.R.N. / Balaram, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ymz.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ymz.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ymz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ymz_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ymz_full_validation.pdf.gz | 476.1 KB | Display | |
Data in XML | 4ymz_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 4ymz_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/4ymz ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ymz | HTTPS FTP |
-Related structure data
Related structure data | 4x22SC 4ywiC 4yxgC 4z0jC 4z0sC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27340.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serovar Icterohaemorrhagiae str. RGA (bacteria) Strain: RGA / Gene: LEP2GSC113_RS0110880 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 References: UniProt: Q8F5I5*PLUS, triose-phosphate isomerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | The reference sequence database derived from str. RGA does not currently exist. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 16% PEG 8000, 1mM Ammonium sulfate, 10mM EDTA, 1mM Sodium azide, 100mM BIS/TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→56.75 Å / Num. all: 58862 / Num. obs: 54809 / % possible obs: 92.7 % / Redundancy: 11.8 % / Biso Wilson estimate: 22.8 Å2 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.87→1.97 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X22 Resolution: 1.87→56.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.278 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→56.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|