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- PDB-1gkj: Histidine Ammonia-Lyase (HAL) Mutant Y280F from Pseudomonas putida -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gkj | |||||||||
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Title | Histidine Ammonia-Lyase (HAL) Mutant Y280F from Pseudomonas putida | |||||||||
![]() | HISTIDINE AMMONIA-LYASE | |||||||||
![]() | LYASE / HISTIDINE DEGRADATION | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Baedeker, M. / Schulz, G.E. | |||||||||
![]() | ![]() Title: Structures of Two Histidine Ammonia-Lyase Modifications and Implications for the Catalytic Mechanism Authors: Baedeker, M. / Schulz, G.E. #1: ![]() 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.8 KB | Display | ![]() |
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PDB format | ![]() | 87.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329.8 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 35.9 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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Unit cell |
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Components
#1: Protein | Mass: 53603.223 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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION CYS273ALA, TYR280PHE. THE 3 RESIDUES ALA 142, SER 143 AND GLY 144 ARE ...CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 Details: CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT PH 8.1. 20 % (V/V) GLYCEROL WERE 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: ![]() |
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: 1.7→19 Å / Num. obs: 64075 / % possible obs: 98 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.6 |
Reflection | *PLUS Lowest resolution: 19 Å / % possible obs: 98 % / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.9 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.7→19 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.7→19 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 19 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.198 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |