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- PDB-2z8j: Crystal Structure of Escherichia coli gamma-Glutamyltranspeptidas... -

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Basic information

Entry
Database: PDB / ID: 2z8j
TitleCrystal Structure of Escherichia coli gamma-Glutamyltranspeptidase in Complex with Azaserine prepared in the dark
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / Azaserine with a diazo group / covalent bond with Thr391 / Acyltransferase / Glutathione biosynthesis / Zymogen
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
O-DIAZOACETYL-L-SERINE / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWada, K. / Irie, M. / Fukuyama, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of Escherichia coli gamma-glutamyltranspeptidase in complex with azaserine and acivicin: novel mechanistic implication for inhibition by glutamine antagonists
Authors: Wada, K. / Hiratake, J. / Irie, M. / Okada, T. / Yamada, C. / Kumagai, H. / Suzuki, H. / Fukuyama, K.
History
DepositionSep 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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)119,0266
Polymers118,6794
Non-polymers3462
Water7,440413
1
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5133
Polymers59,3402
Non-polymers1731
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-79 kcal/mol
Surface area18890 Å2
MethodPISA
2
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5133
Polymers59,3402
Non-polymers1731
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-80 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.260, 126.800, 128.100
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


Mass: 39311.230 Da / Num. of mol.: 2 / Fragment: large chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Plasmid: pSH253 / Production host: Escherichia coli (E. coli) / References: UniProt: P18956, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase


Mass: 20028.475 Da / Num. of mol.: 2 / Fragment: small chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Plasmid: pSH253 / Production host: Escherichia coli (E. coli) / References: UniProt: P18956, gamma-glutamyltransferase
#3: Chemical ChemComp-AZS / O-DIAZOACETYL-L-SERINE / ASASERINE


Type: L-peptide linking / Mass: 173.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 78471 / Num. obs: 78471 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DBU

2dbu


Resolution: 2.05→40.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 78582.09 / 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
Rfree0.267 3925 5.1 %RANDOM
Rwork0.227 ---
obs0.227 77422 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2703 Å2 / ksol: 0.370642 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.4 Å20 Å20 Å2
2---5.1 Å20 Å2
3----4.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8118 0 24 413 8555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 615 4.9 %
Rwork0.272 11855 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2azs.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ggt_final.param

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