[English] 日本語
Yorodumi- PDB-1x90: Crystal structure of mutant form B of a pectin methylesterase inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x90 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mutant form B of a pectin methylesterase inhibitor from Arabidopsis | ||||||
Components | invertase/pectin methylesterase inhibitor family protein | ||||||
Keywords | PROTEIN BINDING / four-helix bundle / alpha hairpin / disulfide bridge / linker / proline / mutant | ||||||
Function / homology | Function and homology information pectinesterase inhibitor activity / pollen tube tip / pollen tube growth / apoplast Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Hothorn, M. / Wolf, S. / Aloy, P. / Greiner, S. / Scheffzek, K. | ||||||
Citation | Journal: Plant Cell / Year: 2004 Title: Structural insights into the target specificity of plant invertase and pectin methylesterase inhibitory proteins Authors: Hothorn, M. / Wolf, S. / Aloy, P. / Greiner, S. / Scheffzek, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x90.cif.gz | 67 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x90.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1x90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x90_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1x90_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 1x90_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1x90_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x90 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x90 | HTTPS FTP |
-Related structure data
Related structure data | 1x8zSC 1x91C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer. The asymmetric unit consists out of two monomers. |
-Components
#1: Protein | Mass: 16303.602 Da / Num. of mol.: 2 / Fragment: residues 1-149 / Mutation: P28A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: APOPLAST-CELL WALL / Gene: AT1G48020 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): origami (DE3) / References: UniProt: Q9LNF2 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 2.5M (NH4)2SO4, 4%(v/v) isopropanol, pH 0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 23, 2004 / Details: bent mirror |
Radiation | Monochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→19.46 Å / Num. all: 7391 / Num. obs: 7391 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.14 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.68→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.56 / Num. unique all: 1184 / % possible all: 93.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X8Z CHAIN A Resolution: 2.68→19.46 Å / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→19.46 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.68→2.85 Å / Rfactor Rfree error: 0.041
|