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Open data
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Basic information
Entry | Database: PDB / ID: 1pe9 | ||||||
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Title | MUTATIONS IN THE T1.5 LOOP OF PECTATE LYASE A | ||||||
![]() | Pectate lyase A | ||||||
![]() | LYASE / PARALLEL BETA HELIX | ||||||
Function / homology | ![]() pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dehdashti, S.J. / Doan, C.N. / Chao, K.L. / Yoder, M.D. | ||||||
![]() | ![]() Title: Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16. Authors: Dehdashti, S.J. / Doan, C.N. / Chao, K.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 | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oocC ![]() 1jtaS 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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Components
#1: Protein | Mass: 38739.535 Da / Num. of mol.: 2 / Mutation: N215S, T217S, S219G, A220S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29155, UniProt: P0C1A2*PLUS, pectate lyase #2: 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: 52.44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000 Monomethyl Ether, 2-[N-Morpholino]Ethanesulfonic Acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2003 |
Radiation | Monochromator: SI 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 100459 / Num. obs: 100459 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.62 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.097 / Net I/σ(I): 29.61 |
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 4.9 / Num. unique all: 7494 / Rsym value: 0.202 / % possible all: 71.2 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. measured all: 564358 / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS % possible obs: 71.2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JTA Resolution: 1.6→36.23 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 328292.99 / Data cutoff high rms absF: 328292.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.3883 Å2 / ksol: 0.353108 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→36.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Num. reflection obs: 94503 / Rfactor Rfree: 0.2132 / Rfactor Rwork: 0.1979 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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