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Open data
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Basic information
Entry | Database: PDB / ID: 3gcb | ||||||
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Title | GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454 | ||||||
![]() | GAL6 | ||||||
![]() | HYDROLASE / BLEOMYCIN HYDROLASE / PEPTIDASE / PROTEASE / DNA-BINDING PROTEIN / SELF-COMPARTMENTALIZING PROTEASE | ||||||
Function / homology | ![]() bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / aminopeptidase activity / cysteine-type peptidase activity / response to toxic substance / double-stranded DNA binding / single-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 / aminopeptidase activity / cysteine-type peptidase activity / response to toxic substance / double-stranded DNA binding / single-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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joshua-Tor, L. / Zheng, W. / Johnston, S.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1a6rC ![]() 1gcbS S: Starting model for refinement C: citing same article ( |
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Similar 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: 53924.270 Da / Num. of mol.: 1 / Mutation: HIS6-TEV-TAG, C73A, DEL(K454) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line: BL21 / Gene: GAL6C73ADELK / Plasmid: PKM260/PLYSS / Species (production host): Escherichia coli / Gene (production host): GAL6C73ADELK / Production host: ![]() ![]() References: UniProt: Q01532, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE AND PEG MME 2K., pH 8.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→35 Å / Num. obs: 49450 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 22 / Rsym value: 0.062 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 199974 |
Reflection shell | *PLUS % possible obs: 96.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GCB Resolution: 1.87→8 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: 40 PROTEIN ATOMS WITH 0 OCCUPANCY BECAUSE OF DISORDERED SIDE CHAINS OCCUPANCIES FOR 40 PROTEIN ATOMS WERE SET TO 0.0 BECAUSE OF DISORDERED SIDE CHAINS. 5 OF THE 17 RESIDUE HIS-TAG/TEV SITE ...Details: 40 PROTEIN ATOMS WITH 0 OCCUPANCY BECAUSE OF DISORDERED SIDE CHAINS OCCUPANCIES FOR 40 PROTEIN ATOMS WERE SET TO 0.0 BECAUSE OF DISORDERED SIDE CHAINS. 5 OF THE 17 RESIDUE HIS-TAG/TEV SITE ARE SEEN IN THE STRUCTURE.
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Displacement parameters | Biso mean: 13.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.94 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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