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- PDB-1jrg: Crystal Structure of the R3 form of Pectate Lyase A, Erwinia chry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jrg | ||||||
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Title | Crystal Structure of the R3 form of Pectate Lyase A, Erwinia chrysanthemi | ||||||
![]() | Pectate lyase | ||||||
![]() | LYASE / parallel beta helix beta elimination | ||||||
Function / homology | ![]() pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomas, L.M. / Doan, C. / Oliver, R.L. / Yoder, M.D. | ||||||
![]() | ![]() Title: Structure of pectate lyase A: comparison to other isoforms. Authors: Thomas, L.M. / Doan, C.N. / Oliver, R.L. / Yoder, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.3 KB | Display | ![]() |
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PDB format | ![]() | 116.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 467.8 KB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 44.1 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38794.609 Da / Num. of mol.: 2 / Fragment: Pectate lyase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29155, UniProt: P0C1A2*PLUS, pectate lyase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8K, PEG1K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 153 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 45453 / Num. obs: 41984 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.077 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.31 / % possible all: 99 |
Reflection | *PLUS Num. obs: 44138 / % possible obs: 98.3 % / Num. measured all: 111710 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PelE search model comprised of residues 30-61, 70-100, 105-251, 258-280, 293-314, and 323-332. (Coordinates provided by F. Jurnak) Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8 /
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.2109 / Rfactor Rwork: 0.1596 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.261 |