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- PDB-5y9b: Crystal structure of Bacillus licheniformis Gamma glutamyl transp... -

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Basic information

Entry
Database: PDB / ID: 5y9b
TitleCrystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with DON
Components(Gamma glutamyl ...) x 2
KeywordsTRANSFERASE / Gamma glutamyl transpeptidase / Bacillus licheniformis / DON
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / metal ion binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-DIAZENYL-5-OXO-L-NORLEUCINE / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGoel, M. / Kumari, S. / Pal, R. / Gupta, R.
CitationJournal: To Be Published
Title: Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine
Authors: Goel, M. / Kumari, S. / Pal, R. / Gupta, R.
History
DepositionAug 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma glutamyl transpeptidase
B: Gamma glutamyl transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3896
Polymers64,0732
Non-polymers3154
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-106 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.560, 61.396, 145.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Gamma glutamyl ... , 2 types, 2 molecules AB

#1: Protein Gamma glutamyl transpeptidase


Mass: 43538.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q65KZ6*PLUS, gamma-glutamyltransferase
#2: Protein Gamma glutamyl transpeptidase


Mass: 20534.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q65KZ6*PLUS, gamma-glutamyltransferase

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Non-polymers , 4 types, 149 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DON / 6-DIAZENYL-5-OXO-L-NORLEUCINE / (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID


Type: L-peptide linking / Mass: 173.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, 100 mM NaCl, 200 mM MgCl2, MPD, 100 mM Tris-Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 29483 / % possible obs: 97.1 % / Redundancy: 10 % / Rpim(I) all: 0.024 / Χ2: 1.18 / Net I/σ(I): 29.39
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 9 % / Mean I/σ(I) obs: 2.73 / Num. unique obs: 1288 / Χ2: 0.91 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data processing
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XLU

5xlu


Resolution: 2.15→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.009 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23609 1532 5.2 %RANDOM
Rwork0.17702 ---
obs0.18026 27909 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å2-0 Å20 Å2
2--1.11 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.15→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 16 145 4265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194218
X-RAY DIFFRACTIONr_bond_other_d0.0020.023807
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9715730
X-RAY DIFFRACTIONr_angle_other_deg1.55338866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96325.193181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34315672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9681515
X-RAY DIFFRACTIONr_chiral_restr0.0970.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1184.0882173
X-RAY DIFFRACTIONr_mcbond_other3.1194.0882172
X-RAY DIFFRACTIONr_mcangle_it4.2986.1192712
X-RAY DIFFRACTIONr_mcangle_other4.2976.1192713
X-RAY DIFFRACTIONr_scbond_it3.2674.2732045
X-RAY DIFFRACTIONr_scbond_other3.2674.2732045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5646.3153017
X-RAY DIFFRACTIONr_long_range_B_refined5.94748.3994710
X-RAY DIFFRACTIONr_long_range_B_other5.94848.3954702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.152→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 86 -
Rwork0.269 1882 -
obs--89.25 %

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