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Yorodumi- PDB-1x8z: Crystal structure of a pectin methylesterase inhibitor from Arabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x8z | ||||||
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Title | Crystal structure of a pectin methylesterase inhibitor from Arabidopsis thaliana | ||||||
Components | invertase/pectin methylesterase inhibitor family protein | ||||||
Keywords | PROTEIN BINDING / four-helix bundle / alpha hairpin / disulfide bridge | ||||||
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: 2.86 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x8z.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x8z.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1x8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x8z_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 1x8z_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 1x8z_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1x8z_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/1x8z ftp://data.pdbj.org/pub/pdb/validation_reports/x8/1x8z | HTTPS FTP |
-Related structure data
Related structure data | 1x90C 1x91C 1rj1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a dimer generated from the molecules chain B and C in the asymmetric unit / The biological assembly is a dimer generated from the molecule chain A and its closest symmetry mate |
-Components
#1: Protein | Mass: 16444.725 Da / Num. of mol.: 3 / Fragment: residues 1-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: APOPLAST-CELL WALL / Gene: AT1G48020 / Plasmid: pETM 20 / Production host: Escherichia coli (E. coli) / Strain (production host): origami (DE3) / References: UniProt: Q9LNF2 #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: 3.05 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10%(v/v) PEG 8000, 0.3M NaCl, 0.1M Na/K Pi, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2003 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→29.06 Å / Num. all: 14136 / Num. obs: 14136 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.91 |
Reflection shell | Resolution: 2.86→3.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2307 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: p(ALA) version of PDB entry 1RJ1 Resolution: 2.86→29.06 Å / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.86→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→3.04 Å / Rfactor Rfree error: 0.032
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