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Yorodumi- PDB-2ntp: Crystal structure of pectin methylesterase in complex with hexasa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ntp | |||||||||
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Title | Crystal structure of pectin methylesterase in complex with hexasaccharide VI | |||||||||
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: 1.7 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ntp.cif.gz | 169.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ntp.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ntp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2ntp ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2ntp | HTTPS FTP |
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-Related structure data
Related structure data | 2nspC 2nstC 2nt6C 2nt9C 2ntbC 2ntqC 1qjvS 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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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.) 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 | methyl alpha-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...methyl alpha-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid | Source method: isolated from a genetically manipulated source #3: Polysaccharide | methyl beta-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...methyl beta-D-galactopyranuronate-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid | Source method: isolated from a genetically manipulated source #4: 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: 2.85 Å3/Da / Density % sol: 56.84 % |
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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: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.9 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Feb 5, 2006 / Details: monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.32 Å / Num. all: 91245 / Num. obs: 91245 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 13.25 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1QJV Resolution: 1.7→36.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.844 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 / 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: 16.201 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→36.32 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: 1.7→1.744 Å / Total num. of bins used: 20
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