[English] 日本語
Yorodumi- PDB-2ntq: Crystal structure of pectin methylesterase in complex with hexasa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ntq | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of pectin methylesterase in complex with hexasaccharide VII | ||||||||||||
Components | Pectinesterase A | ||||||||||||
Keywords | HYDROLASE / PME hexasaccharide complex | ||||||||||||
Function / homology | Function and homology information pectinesterase / pectinesterase activity / : / cell wall modification / pectin catabolic process / cell outer membrane / extracellular space Similarity search - Function | ||||||||||||
Biological species | Erwinia chrysanthemi (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||||||||
Authors | Fries, M. / Brocklehurst, K. / Shevchik, V.E. / Pickersgill, R.W. | ||||||||||||
Citation | Journal: Embo J. / Year: 2007 Title: Molecular basis of the activity of the phytopathogen pectin methylesterase. Authors: Fries, M. / Ihrig, J. / Brocklehurst, K. / Shevchik, V.E. / Pickersgill, R.W. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ntq.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ntq.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 2ntq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2ntq ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2ntq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2nspC 2nstC 2nt6C 2nt9C 2ntbC 2ntpC 1qjvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 25 - 366 / Label seq-ID: 1 - 342
|
-Components
#1: Protein | Mass: 36993.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Strain: 3937 / Gene: pemA, pem / Plasmid: pBCKS/pemA / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 / References: UniProt: P0C1A9, pectinesterase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% v/v Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006 / Details: monochromator |
Radiation | Monochromator: Si(111)/Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→97.13 Å / Num. all: 77283 / Num. obs: 77283 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 12.53 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1QJV Resolution: 1.8→97.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.159 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.013 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→97.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2609 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|