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- PDB-5xlu: High Resolution Crystal Structure of Bacillus Licheniformis Gamma... -

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Basic information

Entry
Database: PDB / ID: 5xlu
TitleHigh Resolution Crystal Structure of Bacillus Licheniformis Gamma Glutamyl Transpeptidase with Acivicin
Components(Gamma glutamyl ...) x 2
KeywordsTRANSFERASE / Gamma glutamyl transpeptidase / Bacillus licheniformis / Acivicin
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 / Glutamine Phosphoribosylpyrophosphate, subunit 1, 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
Chem-AVN / Glutathione hydrolase proenzyme / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKumari, S. / Goel, M. / Gupta, R. / Pal, R.
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of Bacillus Licheniformis Gamma Glutamyl Transpeptidase with Acivicin
Authors: Kumari, S. / Goel, M. / Gupta, R.
History
DepositionMay 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,4025
Polymers64,0912
Non-polymers3113
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-93 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.005, 85.732, 124.664
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: 43556.383 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(DE3) / 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(DE3) / References: UniProt: A9YTT0*PLUS, gamma-glutamyltransferase

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Non-polymers , 4 types, 820 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AVN / (2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID / ACIVICIN


Type: L-peptide linking / Mass: 178.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7ClN2O3 / Comment: inhibitor*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG MME 2000, 200mM magnesium chloride, 100mM Tris-Cl, 5mM acivicin VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→70.64 Å / Num. obs: 92246 / % possible obs: 96.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 24.9 Å2 / Net I/σ(I): 34.01
Reflection shellResolution: 1.45→1.48 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
PHASER2.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OTT

4ott


Resolution: 1.45→70.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.999 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20513 4567 5 %RANDOM
Rwork0.17352 ---
obs0.17508 87318 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.45→70.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 17 817 5002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194307
X-RAY DIFFRACTIONr_bond_other_d0.0020.024039
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9755829
X-RAY DIFFRACTIONr_angle_other_deg1.10439349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99725.078193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39515724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9021519
X-RAY DIFFRACTIONr_chiral_restr0.1420.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214888
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02915
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_it1.3431.3312173
X-RAY DIFFRACTIONr_mcbond_other1.3221.332167
X-RAY DIFFRACTIONr_mcangle_it1.8321.9982709
X-RAY DIFFRACTIONr_mcangle_other1.8321.9992710
X-RAY DIFFRACTIONr_scbond_it2.6391.5732134
X-RAY DIFFRACTIONr_scbond_other2.6391.5722135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7452.2623116
X-RAY DIFFRACTIONr_long_range_B_refined5.8113.4865862
X-RAY DIFFRACTIONr_long_range_B_other5.76113.3545802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 330 -
Rwork0.431 6234 -
obs--93.49 %

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