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- PDB-2e0x: Crystal Structure of Gamma-glutamyltranspeptidase from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 2e0x
TitleCrystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli (monoclinic form)
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / gamma-glutamyltransferase / ggt / gamma-gtp
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, 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 speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOkada, T. / Wada, K. / Fukuyama, K.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism
Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate
Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K.
History
DepositionOct 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,2606
Polymers120,1804
Non-polymers802
Water7,782432
1
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1303
Polymers60,0902
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-90.3 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1303
Polymers60,0902
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-90.7 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.23, 127.9, 75.14
Angle α, β, γ (deg.)90.0, 94.78, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-glutamyltranspeptidase


Mass: 39827.070 Da / Num. of mol.: 2 / Fragment: LARGE SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ggt / Plasmid: PSH1291 / Production host: Escherichia coli (E. coli) / Strain (production host): SH1603 / References: UniProt: P18956, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase


Mass: 20262.951 Da / Num. of mol.: 2 / Fragment: SMALL SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ggt / Plasmid: PSH1291 / Production host: Escherichia coli (E. coli) / Strain (production host): SH1603 / References: UniProt: P18956, gamma-glutamyltransferase
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.5, 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 29, 2006
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 89113 / Num. obs: 89113 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.095 / Χ2: 0.952 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.317 / Num. unique all: 8681 / Χ2: 0.546 / % possible all: 96.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.14 Å31.99 Å
Translation2.14 Å31.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
BSSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A MOLECULE (CHAIN ID A,B) OF THE PDB ENTRY 2DBU

2dbu


Resolution: 1.95→29.91 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.41 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4165 5 %RANDOM
Rwork0.193 ---
all0.195 83076 --
obs0.195 83076 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.965 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8099 0 2 432 8533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228260
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.97111203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03651070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07925.581344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.655151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1311528
X-RAY DIFFRACTIONr_chiral_restr0.0820.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026280
X-RAY DIFFRACTIONr_nbd_refined0.2010.24096
X-RAY DIFFRACTIONr_nbtor_refined0.30.25715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2501
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.27
X-RAY DIFFRACTIONr_mcbond_it0.7151.55477
X-RAY DIFFRACTIONr_mcangle_it1.02928552
X-RAY DIFFRACTIONr_scbond_it1.90533148
X-RAY DIFFRACTIONr_scangle_it2.8784.52651
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 273 -
Rwork0.217 5304 -
obs-5577 84.94 %

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