+Open data
-Basic information
Entry | Database: PDB / ID: 1a6r | ||||||
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Title | GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A | ||||||
Components | GAL6 | ||||||
Keywords | HYDROLASE / BLEOMYCIN HYDROLASE / PEPTIDASE / PROTEASE / DNA-BINDING PROTEIN / SELF-COMPARTMENTALIZING PROTEASE | ||||||
Function / homology | Function and homology information bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cysteine-type peptidase activity / aminopeptidase activity / response to toxic substance / single-stranded DNA binding / double-stranded DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cysteine-type peptidase activity / aminopeptidase activity / response to toxic substance / single-stranded DNA binding / double-stranded DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cysteine-type endopeptidase activity / response to antibiotic / mRNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Joshua-Tor, L. / Zheng, W. / Johnston, S.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: The unusual active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase, and peptide ligase. Authors: Zheng, W. / Johnston, S.A. / Joshua-Tor, L. #1: Journal: Science / Year: 1995 Title: Crystal Structure of a Conserved Protease that Binds DNA: The Bleomycin Hydrolase, Gal6 Authors: Joshua-Tor, L. / Xu, H.E. / Johnston, S.A. / Rees, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6r.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6r.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6r ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6r | HTTPS FTP |
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-Related structure data
Related structure data | 3gcbC 1gcbS S: Starting model for refinement C: citing same article (ref.) |
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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: 54053.449 Da / Num. of mol.: 1 / Mutation: HIS6-TEV-TAG, S2A, C73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: BL21 / Gene: GAL6C73A / Plasmid: PKM260/PLYSS / Species (production host): Escherichia coli / Gene (production host): GAL6C73A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q01532, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Chemical | ChemComp-SO4 / #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: 2.73 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE AND PEG 4K., pH 9.0 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.08 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 37272 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 58 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 31 / Rsym value: 0.164 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 367565 |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GCB Resolution: 2.05→8 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: 46 PROTEIN ATOMS WITH 0 OCCUPANCY BECAUSE OF DISORDERED SIDE CHAINS
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Displacement parameters | Biso mean: 16.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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