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- PDB-4otu: Crystal structure of the gamma-glutamyltranspeptidase from Bacill... -

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Basic information

Entry
Database: PDB / ID: 4otu
TitleCrystal structure of the gamma-glutamyltranspeptidase from Bacillus licheniformis in complex with L-Glutamate
Components
  • Gamma glutamyl transpeptidase
  • Gamma-glutamyltranspeptidase
KeywordsHYDROLASE / Ntn hydrolase
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
GLUTAMIC ACID / Glutathione hydrolase proenzyme / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.022 Å
AuthorsMerlino, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Low resolution X-ray structure of gamma-glutamyltranspeptidase from Bacillus licheniformis: Opened active site cleft and a cluster of acid residues potentially involved in the recognition of a metal ion.
Authors: Lin, L.L. / Chen, Y.Y. / Chi, M.C. / Merlino, A.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_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-glutamyltranspeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2844
Polymers64,1122
Non-polymers1712
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-96 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.627, 60.465, 145.718
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 glutamyl transpeptidase


Mass: 43578.473 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) / References: UniProt: A9YTT0, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase Ggt


Mass: 20533.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: ggt, BL03798, BLi01364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65KZ6, gamma-glutamyltransferase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 3350, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.0, 8.5 mM L-Glu, Protein concentration 10 mg/ml., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 30, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.101
11K, H, -L20.899
ReflectionResolution: 3.022→50 Å / Num. all: 10129 / Num. obs: 10129 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0032phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB code 4OTT

4ott


Resolution: 3.022→27.99 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.775 / SU B: 18.64 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28843 468 4.6 %RANDOM
Rwork0.2017 ---
all0.2057 9625 --
obs0.2057 9625 91.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.335 Å2
Baniso -1Baniso -2Baniso -3
1--19.65 Å2-0 Å2-0 Å2
2--6.52 Å20 Å2
3---13.13 Å2
Refinement stepCycle: LAST / Resolution: 3.022→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 11 1 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194312
X-RAY DIFFRACTIONr_bond_other_d0.0020.024067
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9755835
X-RAY DIFFRACTIONr_angle_other_deg0.83839433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77425.156192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59815740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6321518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
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_it2.5334.5922181
X-RAY DIFFRACTIONr_mcbond_other2.5334.5932180
X-RAY DIFFRACTIONr_mcangle_it4.1876.8862721
X-RAY DIFFRACTIONr_mcangle_other4.1866.8842722
X-RAY DIFFRACTIONr_scbond_it2.0454.7162131
X-RAY DIFFRACTIONr_scbond_other2.0464.7212128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4696.9973115
X-RAY DIFFRACTIONr_long_range_B_refined6.85243.24510498
X-RAY DIFFRACTIONr_long_range_B_other6.85343.25810496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.022→3.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 32 -
Rwork0.284 512 -
obs--69.92 %

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