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- PDB-3gcb: GAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454 -

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Basic information

Entry
Database: PDB / ID: 3gcb
TitleGAL6 (YEAST BLEOMYCIN HYDROLASE) MUTANT C73A/DELTAK454
ComponentsGAL6
KeywordsHYDROLASE / 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 / aminopeptidase activity / cysteine-type peptidase 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 / aminopeptidase activity / cysteine-type peptidase activity / response to toxic substance / single-stranded DNA binding / double-stranded DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to antibiotic / cysteine-type endopeptidase activity / mRNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cysteine proteinase 1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJoshua-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
DepositionFeb 27, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5898
Polymers53,9241
Non-polymers6657
Water7,584421
1
A: GAL6
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)327,53348
Polymers323,5466
Non-polymers3,98742
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area44040 Å2
ΔGint-540 kcal/mol
Surface area99330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.547, 150.547, 90.134
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein GAL6 / YBH / YEAST BLEOMYCIN HYDROLASE


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.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Gene: GAL6C73ADELK / Plasmid: PKM260/PLYSS / Species (production host): Escherichia coli / Gene (production host): GAL6C73ADELK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q01532, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.5 mMbleomycin1drop
325 mMTris-HCl1drop
40.5 Mammonium sulfate1reservoir
53 %(v/v)mPEG20001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCB

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4876 10 %RANDOM
Rwork0.173 ---
obs0.173 48446 99 %-
Displacement parametersBiso mean: 13.4 Å2
Refinement stepCycle: LAST / Resolution: 1.87→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 37 421 4152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shellResolution: 1.87→1.94 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.228 472 10.2 %
Rwork0.198 4149 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_JPL.PROTOPHCSDX_JPL.PRO
X-RAY DIFFRACTION2PARAM19_LJ.SOLTOPH19_MOD.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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