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- PDB-3whq: Crystal structure of gamma-glutamyltranspeptidase from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 3whq
TitleCrystal structure of gamma-glutamyltranspeptidase from Bacillus subtilis (crystal soaked for 0 min. in acivicin soln. )
Components
  • Gamma-glutamyltranspeptidase large chain
  • Gamma-glutamyltranspeptidase small chain
KeywordsHYDROLASE / TRANSFERASE / Glutathione hydrolysis
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / proteolysis / extracellular region
Similarity search - Function
Gamma-glutamyltranspeptidase, small (S) subunit / : / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / : / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 ...Gamma-glutamyltranspeptidase, small (S) subunit / : / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / : / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWada, K. / Fukuyama, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue.
Authors: Ida, T. / Suzuki, H. / Fukuyama, K. / Hiratake, J. / Wada, K.
History
DepositionAug 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase large chain
B: Gamma-glutamyltranspeptidase small chain


Theoretical massNumber of molelcules
Total (without water)66,3162
Polymers66,3162
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-96 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.633, 71.664, 143.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gamma-glutamyltranspeptidase large chain / L-subunit of gamma-glutamyltranspeptidase


Mass: 46286.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ggt, BSU18410 / Plasmid: pCold-I / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P54422, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase
#2: Protein Gamma-glutamyltranspeptidase small chain / S-subunit of gamma-glutamyltranspeptidase


Mass: 20029.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ggt, BSU18410 / Plasmid: pCold-I / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P54422, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: oil batch / pH: 7
Details: 26% (w/v) PEG 3350, 0.7M sodium thiocyanate, 6% (v/v) ethylene glycol, pH 7.0, Oil batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 53570 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V36

2v36


Resolution: 1.85→28.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.448 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21351 2716 5.1 %RANDOM
Rwork0.17598 ---
all0.17784 50760 --
obs0.17784 50760 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 0 458 4643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9735783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61225.414181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22715743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0671515
X-RAY DIFFRACTIONr_chiral_restr0.1170.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22274
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.52781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35224348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28431709
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5754.51435
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 218 -
Rwork0.212 3606 -
obs--98.3 %

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