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

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Basic information

Entry
Database: PDB / ID: 4ott
TitleCrystal structure of the gamma-glutamyltranspeptidase from Bacillus licheniformis.
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
Glutathione hydrolase proenzyme / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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)64,1614
Polymers64,1122
Non-polymers492
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-108 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.896, 61.968, 148.245
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) / Strain: DSM 13 / ATCC 14580 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Protein concentration 20 mg/ml, 20% PEG3350, 0.2 M MgCl2, 0.2 M Tris-HCl, pH 8.2, 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 29, 2013 / Details: mirror
RadiationProtocol: 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, L10.858
11K, H, -L20.142
ReflectionResolution: 2.95→50 Å / Num. all: 11668 / Num. obs: 11668 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3A75

3a75


Resolution: 2.98→26.25 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.831 / SU B: 17.415 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 548 4.6 %RANDOM
Rwork0.1907 ---
all0.19442 11102 --
obs0.19442 11102 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.98→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 2 4 4159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194261
X-RAY DIFFRACTIONr_bond_other_d0.0020.024003
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9715768
X-RAY DIFFRACTIONr_angle_other_deg0.91439281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76425.026191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.21715724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6721518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
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_it1.9333.8182154
X-RAY DIFFRACTIONr_mcbond_other1.933.8182153
X-RAY DIFFRACTIONr_mcangle_it3.1895.7232689
X-RAY DIFFRACTIONr_mcangle_other3.1895.7242690
X-RAY DIFFRACTIONr_scbond_it1.8313.9462107
X-RAY DIFFRACTIONr_scbond_other1.8313.9472108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0995.8423080
X-RAY DIFFRACTIONr_long_range_B_refined5.89636.95411067
X-RAY DIFFRACTIONr_long_range_B_other5.89636.95511068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.982→3.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 25 -
Rwork0.285 589 -
obs--71.31 %

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