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- PDB-1gcb: GAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL) -

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Basic information

Entry
Database: PDB / ID: 1gcb
TitleGAL6, YEAST BLEOMYCIN HYDROLASE DNA-BINDING PROTEASE (THIOL)
ComponentsGAL6 HG (EMTS) DERIVATIVE
KeywordsDNA BINDING PROTEIN / DNA-BINDING / PEPTIDASE / CYSTEINE PROTEASE / REGULATORY FACTOR / BLEOMYCIN HYDROLASE / RING PROTEIN / DNA-BINDING PROTEIN
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 / cysteine-type endopeptidase activity / response to antibiotic / 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 / Resolution: 2.2 Å
AuthorsJoshua-Tor, L. / Xu, H.E. / Johnston, S.A. / Rees, D.C.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Yeast Bleomycin Hydrolase is a DNA-Binding Cysteine Protease: Identification, Purification, Biochemical Characterization
Authors: Xu, H.E. / Johnston, S.A.
History
DepositionJul 18, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET IN THE SHEET RECORDS BELOW STRAND 7 OF SHEET B IS REPEATED IN SHEET C BECAUSE IT TAKES PART ...SHEET IN THE SHEET RECORDS BELOW STRAND 7 OF SHEET B IS REPEATED IN SHEET C BECAUSE IT TAKES PART IN BOTH SHEETS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAL6 HG (EMTS) DERIVATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3359
Polymers52,1521
Non-polymers1,1838
Water4,288238
1
A: GAL6 HG (EMTS) DERIVATIVE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)320,01054
Polymers312,9146
Non-polymers7,09648
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 area42180 Å2
ΔGint-742 kcal/mol
Surface area95990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.150, 151.150, 89.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: CIS PROLINE - PRO 63 / 2: CIS PROLINE - PRO 328
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 2 .. 453 IDENTITY MATRIX SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 2 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: 2 .. 453 MONOMER 2 OF HEXAMER SYMMETRY1 3 0.000000 -1.000000 0.000000 1.00000 SYMMETRY2 3 1.000000 -1.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 4 -0.500000 -0.866000 0.000000 151.15000 SYMMETRY2 4 0.866000 -0.500000 0.000000 0.00000 SYMMETRY3 4 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: 2 .. 453 MONOMER 3 OF HEXAMER SYMMETRY1 5 -1.000000 1.000000 0.000000 1.00000 SYMMETRY2 5 -1.000000 0.000000 0.000000 1.00000 SYMMETRY3 5 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 6 -0.500000 0.866000 0.000000 75.58000 SYMMETRY2 6 -0.866000 -0.500000 0.000000 130.90000 SYMMETRY3 6 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: 2 .. 453 MONOMER 4 OF HEXAMER SYMMETRY1 7 0.000000 -1.000000 0.000000 1.00000 SYMMETRY2 7 -1.000000 0.000000 0.000000 1.00000 SYMMETRY3 7 0.000000 0.000000 -1.000000 0.50000 SYMMETRY1 8 0.500000 -0.866000 0.000000 75.58000 SYMMETRY2 8 -0.866000 -0.500000 0.000000 130.90000 SYMMETRY3 8 0.000000 0.000000 -1.000000 44.94000 APPLIED TO RESIDUES: 2 .. 453 MONOMER 5 OF HEXAMER (DIMER PARTNER OF MONOMER 1) SYMMETRY1 9 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 9 1.000000 -1.000000 0.000000 0.00000 SYMMETRY3 9 0.000000 0.000000 -1.000000 0.50000 SYMMETRY1 10 0.500000 0.866000 0.000000 0.00000 SYMMETRY2 10 0.866000 -0.500000 0.000000 0.00000 SYMMETRY3 10 0.000000 0.000000 -1.000000 44.94000 APPLIED TO RESIDUES: 2 .. 453 MONOMER 6 OF HEXAMER SYMMETRY1 11 -1.000000 1.000000 0.000000 1.00000 SYMMETRY2 11 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 11 0.000000 0.000000 -1.000000 0.50000 SYMMETRY1 12 -1.000000 0.000000 0.000000 151.15000 SYMMETRY2 12 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 12 0.000000 0.000000 -1.000000 44.94000

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Components

#1: Protein GAL6 HG (EMTS) DERIVATIVE


Mass: 52152.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: SC277 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01532
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
136 mg/mlprotein1drop
225 mMTris-HCl1drop
310 %glycerol1drop
421 %PEG40001reservoir
50.3 Mammonium sulfate1reservoir
62 mMDTT1reservoir
7100 mMTris-HCl1reservoir

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL7-111.08
21.54
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
RIGAKU RAXIS II2IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.541
ReflectionResolution: 2.2→20 Å / Num. obs: 31451 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.074
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 202481 / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MSCdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 0
Details: FOR RESIDUE LEU 452 THE ELECTRON DENSITY IS LARGER THAN EXPECTED.
RfactorNum. reflection% reflection
Rfree0.274 -10 %
Rwork0.209 --
obs0.209 30018 -
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 25 238 3916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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