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Yorodumi- PDB-1eb4: Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eb4 | |||||||||
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Title | Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida | |||||||||
Components | HISTIDINE AMMONIA-LYASE | |||||||||
Keywords | LYASE / AMMONIA-LYASE / HISTIDINE DEGRADATION | |||||||||
Function / homology | Function and homology information histidine ammonia-lyase / histidine ammonia-lyase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / cytoplasm Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2 Å | |||||||||
Authors | Baedeker, M. / Schulz, G.E. | |||||||||
Citation | Journal: Structure / Year: 2002 Title: Autocatalytic Peptide Cyclization During Chain Folding of Histidine Ammonia-Lyase. Authors: Baedeker, M. / Schulz, G.E. #1: Journal: Biochemistry / Year: 1999 Title: Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile Authors: Schwede, T.F. / Retey, J. / Schulz, G.E. #2: Journal: Protein Eng. / Year: 1999 Title: Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue Authors: Schwede, T.F. / Baedeker, M. / Langer, M. / Retey, J. / Schulz, G.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eb4.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eb4.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 1eb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eb4_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 1eb4_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 1eb4_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 1eb4_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1eb4 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1eb4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53543.129 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP (MDO).THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS ...Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP (MDO).THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS DELETED. THE SIDE CHAIN OF SER 143 IS DEHYDRATED. Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Cellular location: CYTOPLASM / Gene: HUTH / Plasmid: PT7-7H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21310, histidine ammonia-lyase | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDHas protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 Details: 2.0 M (NH4)2 SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL USED AS CRYOPROTECTANT | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3.85 / Method: vapor diffusion, hanging drop / Details: Schwede, T.F., (1999) Protein Eng., 12, 151. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUB200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 39112 / % possible obs: 96 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.4 |
Reflection | *PLUS Rmerge(I) obs: 0.134 |
Reflection shell | *PLUS % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELX / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.171 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |