+Open data
-Basic information
Entry | Database: PDB / ID: 1ru4 | ||||||
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Title | Crystal structure of pectate lyase Pel9A | ||||||
Components | Pectate lyase | ||||||
Keywords | LYASE / Parallel beta-helix | ||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / pectin catabolic process / : / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Erwinia chrysanthemi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Jenkins, J. / Shevchik, V.E. / Hugouvieux-Cotte-Pattat, N. / Pickersgill, R.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi Authors: Jenkins, J. / Shevchik, V.E. / Hugouvieux-Cotte-Pattat, N. / 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 | 1ru4.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ru4.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 1ru4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ru4_validation.pdf.gz | 411.3 KB | Display | wwPDB validaton report |
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Full document | 1ru4_full_validation.pdf.gz | 412.8 KB | Display | |
Data in XML | 1ru4_validation.xml.gz | 21 KB | Display | |
Data in CIF | 1ru4_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/1ru4 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/1ru4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42827.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: PelL / Production host: Escherichia coli (E. coli) References: UniProt: Q47473, UniProt: P0C1A7*PLUS, pectate lyase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.4 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 12% PEG 3350,100mM sodium chloride, 400mM citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38 Å / Num. all: 49456 / Num. obs: 49017 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.124 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→38 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→38 Å
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Refine LS restraints |
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