+Open data
-Basic information
Entry | Database: PDB / ID: 1c7g | ||||||
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Title | TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA | ||||||
Components | TYROSINE PHENOL-LYASE | ||||||
Keywords | LYASE / TYROSINE DEGRADATION / PYRIDOXAL 5'-PHOSPHATE DEPENDENT | ||||||
Function / homology | Function and homology information tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Pantoea agglomerans pv. gypsophilae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mikami, B. / Yamamoto, Y. / Katayama, T. / Suzuki, H. | ||||||
Citation | Journal: To be Published Title: The Structure of Tyrosine Phenol-Lyase from Erwinia Herbicola Authors: Mikami, B. / Yamamoto, Y. / Katayama, T. / Suzuki, H. / Kumagai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c7g.cif.gz | 321.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c7g.ent.gz | 254.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c7g_validation.pdf.gz | 417.3 KB | Display | wwPDB validaton report |
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Full document | 1c7g_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 1c7g_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 1c7g_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c7g ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c7g | HTTPS FTP |
-Related structure data
Related structure data | 1tplS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51429.629 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PYRIDOXAL 5'-PHOSPHATE LINK TO A 257, B 257, C 257 AND D 257 Source: (gene. exp.) Pantoea agglomerans pv. gypsophilae (bacteria) Species: Pantoea agglomerans / Strain: pv. gypsophilae / Description: RECOMBINANT GENE / Variant: AJ2985 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / Variant (production host): TNA DEFICIENT / References: UniProt: P31011, tyrosine phenol-lyase #2: Chemical | ChemComp-PLP / #3: 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: 2.3 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 6.2 Details: 30% PEG6000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 6.2 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998 |
Radiation | Monochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.007→42 Å / Num. obs: 113432 / % possible obs: 90.31 % / Observed criterion σ(I): 1 / Redundancy: 4.59 % / Rsym value: 0.102 / Net I/σ(I): 1.34 |
Reflection shell | Resolution: 2.007→2.079 Å / % possible all: 53.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TPL Resolution: 2.1→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 19.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 22 Å / Luzzati d res low obs: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8
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Xplor file |
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