+Open data
-Basic information
Entry | Database: PDB / ID: 1s2t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Apo Phosphoenolpyruvate Mutase | ||||||
Components | Phosphoenolpyruvate phosphomutase | ||||||
Keywords | ISOMERASE / phosphoenolpyruvate mutase / PEP mutase / phosphonopyruvate / phosphonate biosynthesis pathway | ||||||
Function / homology | Function and homology information phosphoenolpyruvate mutase / phosphoenolpyruvate mutase activity / organic phosphonate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Mytilus edulis (blue mussel) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Conformational Flexibility of PEP Mutase Authors: Liu, S. / Lu, Z. / Han, Y. / Jia, Y. / Howard, A. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS ...SEQUENCE THE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS WITH THE SWISS PROT SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1s2t.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1s2t.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 1s2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s2t_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1s2t_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 1s2t_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1s2t_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/1s2t ftp://data.pdbj.org/pub/pdb/validation_reports/s2/1s2t | HTTPS FTP |
-Related structure data
Related structure data | 1s2uC 1s2vC 1s2wC 1pymS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | PEP mutase biological unit is a tetramer. The second part of biological assembly can be generated by the two fold axis : 1-x, y, 1/2-z. |
-Components
#1: Protein | Mass: 32954.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mytilus edulis (blue mussel) / Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56839, phosphoenolpyruvate mutase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
---|---|
Crystal grow | Temperature: 302 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 302K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 40649 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 6.79 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.99→2.06 Å / Rmerge(I) obs: 0.136 / % possible all: 85.4 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1pym Resolution: 2→39.1 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.1 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|