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Open data
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Basic information
Entry | Database: PDB / ID: 1idk | ||||||
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Title | PECTIN LYASE A | ||||||
![]() | PECTIN LYASE A | ||||||
![]() | LYASE / GLYCOPROTEIN / MULTIGENE FAMILY | ||||||
Function / homology | ![]() pectin lyase / pectin lyase activity / pectate lyase activity / polysaccharide catabolic process / cell wall organization / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mayans, O. / Scott, M. / Connerton, I. / Gravesen, T. / Benen, J. / Visser, J. / Pickersgill, R. / Jenkins, J. | ||||||
![]() | ![]() Title: Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Authors: Mayans, O. / Scott, M. / Connerton, I. / Gravesen, T. / Benen, J. / Visser, J. / Pickersgill, R. / Jenkins, J. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Pectin Lyase a from Aspergillus Niger Authors: Jenkins, J. / Scott, M. / Mayans, O. / Pickersgill, R. / Harris, G. / Connerton, I. / Gravesen, T. #2: ![]() Title: The Structure of Bacillus Subtilis Pectate Lyase in Complex with Calcium Authors: Pickersgill, R. / Jenkins, J. / Harris, G. / Nasser, W. / Robert-Baudouy, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 37982.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SECRETED PROTEIN / Source: (natural) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 28% PEG 4000, 100 MM SODIUM ACETATE, 100 MM TRIS-HCL AT PH 8.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Jenkins, J., (1996) Acta Crystallogr.,Sect.D, 52, 402. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 9, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→25.44 Å / Num. obs: 25695 / % possible obs: 94 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.47 |
Reflection shell | Resolution: 1.93→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.3 / % possible all: 72.3 |
Reflection | *PLUS Num. measured all: 80561 |
Reflection shell | *PLUS % possible obs: 84.3 % |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: DERIVED FROM BACILLUS SUBTILIS PECTATE LYASE Resolution: 1.93→15 Å / Cross valid method: FREE R + R VALUE OF SECOND CRYSTAL FORM / σ(F): 2 Details: OVERALL ANISOTROPIC SCALING, BULK SOLVENT CORRECTION AND RESTRAINED ISOTROPIC INDIVIDUAL TEMPERATURE FACTOR REFINEMENT
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Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.97 Å
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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