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- PDB-2e0y: Crystal structure of the samarium derivative of mature gamma-glut... -

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Basic information

Entry
Database: PDB / ID: 2e0y
TitleCrystal structure of the samarium derivative of mature gamma-glutamyltranspeptidase from Escherichia coli
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / gamma-glutamyltransferase / ggt / gamma-gt / glutathione
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 ...: / 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
SAMARIUM (III) ION / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 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: Non-polymer description / Version format compliance
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)120,94111
Polymers120,1804
Non-polymers7617
Water10,359575
1
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5176
Polymers60,0902
Non-polymers4274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-88.2 kcal/mol
Surface area19230 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4255
Polymers60,0902
Non-polymers3353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-89.6 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.92, 125.9, 128.9
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 4000, 0.2M calcium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 84609 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.065
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 5.1 % / Num. unique all: 16196 / Rsym value: 0.285 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DBU

2dbu


Resolution: 2.02→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 71919.617 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4237 5.1 %RANDOM
Rwork0.195 ---
all0.196 83871 --
obs0.196 83871 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.254 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å20 Å2
2---1.53 Å20 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8099 0 32 575 8706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 670 4.9 %
Rwork0.221 12869 -
all0.223 13539 -
obs-13539 96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ggt_final.paramion.top
X-RAY DIFFRACTION4ion.paramggt_final.top

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