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- PDB-2nqo: Crystal Structure of Helicobacter pylori gamma-Glutamyltranspeptidase -

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Basic information

Entry
Database: PDB / ID: 2nqo
TitleCrystal Structure of Helicobacter pylori gamma-Glutamyltranspeptidase
Components(Gamma-glutamyltranspeptidase) x 2
KeywordsTRANSFERASE / Ntn-hydrolase / glutamyltranspeptidase
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / negative regulation of cell cycle G1/S phase transition / glutathione biosynthetic process / negative regulation of T cell proliferation / positive regulation of interleukin-8 production
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBoanca, G. / Sand, A. / Okada, T. / Suzuki, H. / Kumagai, H. / Fukuyama, K. / Barycki, J.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Autoprocessing of Helicobacter pylori gamma-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad.
Authors: Boanca, G. / Sand, A. / Okada, T. / Suzuki, H. / Kumagai, H. / Fukuyama, K. / Barycki, J.J.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 400 COMPOUND THE ASYMMETRIC UNIT CONTAINS A HETEROTETRAMER WHICH IS FORMED FROM TWO COMPLETE ... COMPOUND THE ASYMMETRIC UNIT CONTAINS A HETEROTETRAMER WHICH IS FORMED FROM TWO COMPLETE POLYPEPTIDE CHAINS THAT UNDERGO AUTOPROCESSING (CHAIN BREAKING BETWEEN RESIDUES 379 AND 380). THIS CHAIN BREAKING LEADS TO ACTIVATION OF THE ENZYME. AUTHOR STATES, THAT EXCEPT BEING A TRANSFERASE, THIS ENZYME IS ALSO A HYDROLASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)121,8334
Polymers121,8334
Non-polymers00
Water10,629590
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Gamma-glutamyltranspeptidase
D: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)60,9162
Polymers60,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-72 kcal/mol
Surface area20030 Å2
MethodPISA, PQS
3
A: Gamma-glutamyltranspeptidase
B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)60,9162
Polymers60,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-70 kcal/mol
Surface area19680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.354, 105.206, 91.060
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-glutamyltranspeptidase / Ggt


Mass: 40506.305 Da / Num. of mol.: 2 / Fragment: Residues 27-379 / Mutation: Engineered N-terminal histidine tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: O25743, gamma-glutamyltransferase
#2: Protein Gamma-glutamyltranspeptidase / Ggt


Mass: 20410.186 Da / Num. of mol.: 2 / Fragment: Residues 380-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1118 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: O25743, gamma-glutamyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM HEPES, 25% PEG MME2000, 5 mg/mL protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 72974 / Num. obs: 72974 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.046 / Χ2: 1.035 / Net I/σ(I): 32.3
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.466 / Num. unique all: 7605 / Χ2: 1.211 / % possible all: 77.6

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DBU

2dbu


Resolution: 1.9→28.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 163846.344 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 7385 10.1 %RANDOM
Rwork0.197 ---
all-72974 --
obs-72974 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.788 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å21.81 Å2
2--0.44 Å20 Å2
3---0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8089 0 0 590 8679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 1024 9.9 %
Rwork0.247 9371 -
obs-10395 77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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