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- PDB-2nt9: Crystal structure of pectin methylesterase D178A mutant in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nt9 | ||||||||||||
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Title | Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide IV | ||||||||||||
![]() | Pectinesterase A | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 163.6 KB | Display | ![]() |
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PDB format | ![]() | 126.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2nspC ![]() 2nstC ![]() 2nt6C ![]() 2ntbC ![]() 2ntpC ![]() 2ntqC ![]() 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: 36949.785 Da / Num. of mol.: 2 / Mutation: D178A 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: 2.91 Å3/Da / Density % sol: 57.68 % |
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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![]() |
Reflection | Resolution: 1.9→64.15 Å / Num. all: 59470 / Num. obs: 59470 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 14.95 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.5 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1QJV Resolution: 1.9→44.37 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.038 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.139 / 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: 17.391 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.37 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: 2606 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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