[English] 日本語
![](img/lk-miru.gif)
- PDB-5c1e: Crystal Structure of the Pectin Methylesterase from Aspergillus n... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5c1e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84) | ||||||
![]() | Pectinesterase | ||||||
![]() | HYDROLASE / parallel beta helix / pectin methylesterase | ||||||
Function / homology | ![]() pectinesterase / pectinesterase activity / : / cell wall modification / pectin catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Protein deglycosylated with EndoHf to leave an Asn84 N-linked N-acetylglycosamine stub | ||||||
![]() | Jameson, G.B. / Williams, M.A.K. / Loo, T.S. / Kent, L.M. / Melton, L.D. / Mercadante, D. | ||||||
![]() | ![]() Title: Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control. Authors: Kent, L.M. / Loo, T.S. / Melton, L.D. / Mercadante, D. / Williams, M.A. / Jameson, G.B. #1: ![]() Title: Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions Authors: Mercadante, D. / Melton, L.D. / Jameson, G.B. / Williams, M.A.K. #2: ![]() Title: Substrate Dynamics in Enzyme Action: Rotations of Monosaccharide Subunits in the Binding Groove are Essential for Pectin Methylesterase Processivity Authors: Mercadante, D. / Melton, L.D. / Jameson, G.B. / Williams, M.A.K. / De Simone, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 136.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 481.8 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c1cC ![]() 1xg2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | Monomer according to Gel filtration |
-
Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 31792.287 Da / Num. of mol.: 1 / Fragment: N-terminal truncated exported protein Source method: isolated from a genetically manipulated source Details: After purification, protein was deglycosylated with PNGaseF Source: (gene. exp.) ![]() ![]() Strain: van Tieghem, anamorph / Gene: ASPNIDRAFT_214857 / Plasmid: pYES2 / Production host: ![]() ![]() |
---|---|
#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 335 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.9 M ammonium sulfate, 100 mM sodium acetate, pH 3.6 |
-Data collection
Diffraction | Mean temperature: 123 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 4, 2013 / Details: AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC |
Radiation | Monochromator: AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.16 Å / Num. all: 36656 / Num. obs: 36656 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.94 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.084 / Net I/av σ(I): 8.3 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.1 / % possible all: 89.6 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1xg2 Resolution: 1.75→36.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1975 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8722 / SU B: 4.407 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1049 / SU Rfree: 0.1022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 61.96 Å2 / Biso mean: 20.727 Å2 / Biso min: 12.39 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→36.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -19.2157 Å / Origin y: 25.7632 Å / Origin z: 12.2763 Å
|