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- PDB-2z8i: Crystal Structure of Escherichia coli Gamma-Glutamyltranspeptidas... -

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Basic information

Entry
Database: PDB / ID: 2z8i
TitleCrystal Structure of Escherichia coli Gamma-Glutamyltranspeptidase in Complex with Azaserine
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / Thr391 formed a covalent bond with azaserine / Acyltransferase / Glutathione biosynthesis / Zymogen
Function / homology
Function and homology information


amino acid salvage / gamma-glutamyl-peptidase activity / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione gamma-glutamate hydrolase / 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: 1.65 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 30, 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
Water8,521473
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 area12290 Å2
ΔGint-79 kcal/mol
Surface area19140 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 area12180 Å2
ΔGint-79 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.510, 126.200, 129.200
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 / Comment: antineoplastic, antibiotic, antagonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
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: Nov 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 147754 / Num. obs: 147754 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.312 / % possible all: 96.7

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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: 1.65→29.41 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 183527.77 / 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
Rfree0.236 7013 5.1 %RANDOM
Rwork0.22 ---
obs0.22 138769 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1222 Å2 / ksol: 0.390495 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.94 Å20 Å20 Å2
2---2.76 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 20 473 8602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.29
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: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 1047 4.9 %
Rwork0.267 20464 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2azx.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ligands-cispep.param

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