+Open data
-Basic information
Entry | Database: PDB / ID: 1b8f | |||||||||
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Title | Histidine ammonia-lyase (HAL) 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Schwede, T.F. / Schulz, G.E. | |||||||||
Citation | 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. #1: Journal: Protein Eng. / Year: 1999 Title: Homogenization and crystallization of histidine ammonia-lyase by exchange of a surface cysteine residue. Authors: Schwede, T.F. / Badeker, 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 | 1b8f.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8f.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8f_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 1b8f_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 1b8f_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1b8f_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8f ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8f | 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: 53619.223 Da / Num. of mol.: 1 / Mutation: C273A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Cellular location: CYTOPLASM / Gene: hutH / Plasmid: PT7-7H / Cellular location (production host): CYTOPLASM / 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 15, 1998 |
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: 2.1→39 Å / Num. obs: 28972 / % possible obs: 83 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 8.2 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3 / Rsym value: 18.2 / % possible all: 66 |
Reflection | *PLUS Num. measured all: 82830 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 66 % / Rmerge(I) obs: 0.182 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HISTIDASE IN SPACE GROUP P21 (NOT DEPOSITED) Resolution: 2.1→39 Å / SU B: 5.17 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 39 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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