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- PDB-2ntq: Crystal structure of pectin methylesterase in complex with hexasa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ntq | ||||||||||||
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Title | Crystal structure of pectin methylesterase in complex with hexasaccharide VII | ||||||||||||
![]() | Pectinesterase A | ||||||||||||
![]() | HYDROLASE / PME hexasaccharide complex | ||||||||||||
Function / homology | ![]() pectinesterase / pectinesterase activity / : / cell wall modification / pectin catabolic process / cell outer membrane / extracellular space Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Fries, M. / Brocklehurst, K. / Shevchik, V.E. / Pickersgill, R.W. | ||||||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.3 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 884 KB | Display | ![]() |
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Full document | ![]() | 888 KB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nspC ![]() 2nstC ![]() 2nt6C ![]() 2nt9C ![]() 2ntbC ![]() 2ntpC ![]() 1qjvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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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
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Components
#1: Protein | Mass: 36993.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.8→97.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2609 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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