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- PDB-5b5t: Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidas... -

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Basic information

Entry
Database: PDB / ID: 5b5t
TitleCrystal Structure of Escherichia coli Gamma-Glutamyltranspeptidase in Complex with peptidyl phosphonate inhibitor 1b
Components
  • Gamma-glutamyltranspeptidase large chain
  • Gamma-glutamyltranspeptidase small chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / glutathione / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


amino acid salvage / gamma-glutamyl-peptidase activity / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / self proteolysis / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
: / 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 / Nucleophile aminohydrolases, N-terminal / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6FY / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWada, K. / Fukuyama, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT Japan
CitationJournal: Bioorg.Med.Chem. / Year: 2016
Title: Phosphonate-based irreversible inhibitors of human gamma-glutamyl transpeptidase (GGT). GGsTop is a non-toxic and highly selective inhibitor with critical electrostatic interaction with an ...Title: Phosphonate-based irreversible inhibitors of human gamma-glutamyl transpeptidase (GGT). GGsTop is a non-toxic and highly selective inhibitor with critical electrostatic interaction with an active-site residue Lys562 for enhanced inhibitory activity
Authors: Kamiyama, A. / Nakajima, M. / Han, L. / Wada, K. / Mizutani, M. / Tabuchi, Y. / Kojima-Yuasa, A. / Matsui-Yuasa, I. / Suzuki, H. / Fukuyama, K. / Watanabe, B. / Hiratake, J.
History
DepositionMay 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Aug 11, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase large chain
B: Gamma-glutamyltranspeptidase small chain
C: Gamma-glutamyltranspeptidase large chain
D: Gamma-glutamyltranspeptidase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3808
Polymers118,6794
Non-polymers7014
Water22,9511274
1
A: Gamma-glutamyltranspeptidase large chain
B: Gamma-glutamyltranspeptidase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6904
Polymers59,3402
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-88 kcal/mol
Surface area18810 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase large chain
D: Gamma-glutamyltranspeptidase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6904
Polymers59,3402
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-89 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.990, 126.388, 129.075
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 / Glutathione hydrolase / Gamma-glutamyltranspeptidase Large-subunit


Mass: 39311.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ggt, b3447, JW3412 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P18956, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase
#2: Protein Gamma-glutamyltranspeptidase small chain / Glutathione hydrolase / Gamma-glutamyltranspeptidase Small-subunit


Mass: 20028.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ggt, b3447, JW3412 / Production host: Escherichia coli (E. coli)
References: UniProt: P18956, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase
#3: Chemical ChemComp-6FY / (2~{S})-2-azanyl-4-[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-butan-2-yl]oxyphosphonoyl-butanoic acid


Mass: 310.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H19N2O7P
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1274 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 12.5-17.5% PEG 4000, 0.2M CaCl2, 0.1M Tris-HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 135141 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.5
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.56

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DBU

2dbu


Resolution: 1.7→37.329 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.1936 6679 4.94 %
Rwork0.1781 --
obs0.1789 135104 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8102 0 42 1274 9418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078300
X-RAY DIFFRACTIONf_angle_d0.9511256
X-RAY DIFFRACTIONf_dihedral_angle_d14.4445024
X-RAY DIFFRACTIONf_chiral_restr0.0551254
X-RAY DIFFRACTIONf_plane_restr0.0051486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6975-1.71680.33271770.28543157X-RAY DIFFRACTION72
1.7168-1.7370.2941920.28783398X-RAY DIFFRACTION77
1.737-1.75820.30981920.26153553X-RAY DIFFRACTION81
1.7582-1.78040.25871820.2523819X-RAY DIFFRACTION86
1.7804-1.80390.29872160.25843975X-RAY DIFFRACTION90
1.8039-1.82860.30211820.24144238X-RAY DIFFRACTION95
1.8286-1.85470.26542180.22894472X-RAY DIFFRACTION100
1.8547-1.88240.23992000.2244420X-RAY DIFFRACTION100
1.8824-1.91180.24212020.21774442X-RAY DIFFRACTION99
1.9118-1.94310.2282180.20224425X-RAY DIFFRACTION99
1.9431-1.97660.20732600.20394362X-RAY DIFFRACTION100
1.9766-2.01260.23262210.20444450X-RAY DIFFRACTION99
2.0126-2.05130.20652320.20194406X-RAY DIFFRACTION99
2.0513-2.09320.21342320.19084389X-RAY DIFFRACTION99
2.0932-2.13870.21982070.18064396X-RAY DIFFRACTION99
2.1387-2.18840.20332310.17734383X-RAY DIFFRACTION98
2.1884-2.24310.19432240.17564371X-RAY DIFFRACTION98
2.2431-2.30380.19862470.17884383X-RAY DIFFRACTION98
2.3038-2.37160.22092790.17954345X-RAY DIFFRACTION99
2.3716-2.44810.17472390.18154333X-RAY DIFFRACTION98
2.4481-2.53560.22212600.18594355X-RAY DIFFRACTION98
2.5356-2.63710.19261980.18394395X-RAY DIFFRACTION98
2.6371-2.7570.1892350.17734386X-RAY DIFFRACTION98
2.757-2.90230.18762250.17124383X-RAY DIFFRACTION98
2.9023-3.08410.17272220.17294427X-RAY DIFFRACTION98
3.0841-3.32210.17692410.16514433X-RAY DIFFRACTION99
3.3221-3.65620.15892080.15934499X-RAY DIFFRACTION99
3.6562-4.18460.16092690.1444505X-RAY DIFFRACTION99
4.1846-5.26980.15532410.1364578X-RAY DIFFRACTION100
5.2698-37.33770.17552290.17624747X-RAY DIFFRACTION99

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