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- PDB-2e0w: T391A precursor mutant protein of gamma-Glutamyltranspeptidase fr... -

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Basic information

Entry
Database: PDB / ID: 2e0w
TitleT391A precursor mutant protein of gamma-Glutamyltranspeptidase from Escherichia coli
ComponentsGamma-glutamyltranspeptidase
KeywordsTRANSFERASE / Ntn hydrolase / precursor / gamma-gtp / post-translational processing / maturation
Function / homology
Function and homology information


amino acid salvage / gamma-glutamyl-peptidase activity / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / self proteolysis / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
: / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOkada, T. / Wada, K. / Fukuyama, K.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the gamma-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism
Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate
Authors: Okada, T. / Suzuki, H. / Wada, K. / Kumagai, H. / Fukuyama, K.
History
DepositionOct 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,5832
Polymers118,5832
Non-polymers00
Water95553
1
A: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)59,2921
Polymers59,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-glutamyltranspeptidase


Theoretical massNumber of molelcules
Total (without water)59,2921
Polymers59,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.6, 134.6, 118.4
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Gamma-glutamyltranspeptidase / Gamma-glutamyltransferase large subunit and small subunit


Mass: 59291.562 Da / Num. of mol.: 2 / Mutation: T391A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ggt / Plasmid: pT391A / Production host: Escherichia coli (E. coli) / Strain (production host): SH641 / References: UniProt: P18956, gamma-glutamyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 4000, 10% iso-propanol, 0.1M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 33506 / Num. obs: 33506 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12 % / Rmerge(I) obs: 0.092 / Χ2: 1.066 / Net I/σ(I): 11.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.314 / Num. unique all: 3262 / Χ2: 0.91 / % possible all: 91.9

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Phasing

Phasing MRRfactor: 0.46 / Cor.coef. Fo:Fc: 0.578
Highest resolutionLowest resolution
Rotation3 Å37.35 Å
Translation3 Å37.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A MOLECULE (CHAIN ID A,B) OF PDB ENTRY 2DBU

2dbu


Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.594 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1521 4.9 %RANDOM
Rwork0.217 ---
all0.22 30764 --
obs0.22 30764 92.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7415 0 0 53 7468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227556
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.96710259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76125.461304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.151151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8151525
X-RAY DIFFRACTIONr_chiral_restr0.0860.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025727
X-RAY DIFFRACTIONr_nbd_refined0.2140.23986
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.28
X-RAY DIFFRACTIONr_mcbond_it0.4021.55048
X-RAY DIFFRACTIONr_mcangle_it0.70527874
X-RAY DIFFRACTIONr_scbond_it1.02232840
X-RAY DIFFRACTIONr_scangle_it1.6154.52385
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 97 -
Rwork0.24 1953 -
obs-2050 85.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1188-0.19441.01291.4838-0.392.1101-0.08090.0769-0.007-0.00470.03140.2073-0.1738-0.08610.0494-0.1877-0.00730.0484-0.0412-0.03620.0952-14.69638.6195.835
22.30370.73-0.00561.6789-0.39021.2907-0.14850.5890.0355-0.18570.0997-0.0432-0.1143-0.03290.0487-0.1669-0.01330.00720.0653-0.0386-0.0295-11.77240.466-8.096
32.2567-0.40451.17212.8933-1.61051.6040.19520.0925-1.07010.10030.1411-0.11940.323-0.2618-0.3363-0.1625-0.0128-0.0007-0.1211-0.12470.4874-13.210.7786.575
41.6255-0.59611.12785.20760.69281.02790.19160.1411-0.6583-0.198-0.03940.5880.5185-0.0801-0.1522-0.1195-0.03510.0435-0.0509-0.19730.4032-18.8286.1720.961
51.75990.70470.14011.1816-1.38362.3642-0.18490.4258-0.4426-0.1401-0.2025-0.0510.05770.05920.3875-0.16460.01350.02830.089-0.05830.0602-10.49336.165-6.189
61.9726-0.14460.49141.2819-0.18390.97960.08650.1449-0.4520.0743-0.07110.00430.0357-0.0016-0.0154-0.171-0.01510.028-0.0584-0.06990.2498-8.74323.1948.372
72.63190.33861.02690.56570.77781.60480.007-0.0841-0.1547-0.0038-0.0548-0.1286-0.09450.05720.0478-0.1577-0.01710.0062-0.03770.02130.160316.73541.28722.143
82.8586-0.00480.38141.64390.30051.0232-0.006-0.68420.18020.1094-0.0003-0.1505-0.05630.04320.0063-0.2348-0.0083-0.03010.03620.0195-0.021113.83742.77232.854
99.01675.0160.446713.59021.05140.08180.3407-0.9103-0.90821.1838-0.2214-0.24940.7667-0.1078-0.11930.01680.0409-0.1330.08280.39150.187818.74317.8437.951
102.87990.86211.05055.1614-0.570.6550.3172-0.7391-0.63690.9327-0.1723-0.55720.1572-0.0609-0.1448-0.0761-0.0011-0.20310.0560.30550.293119.4416.07736.399
115.5351-0.4331-1.09011.82841.89332.4330.0224-0.4342-0.13540.0681-0.0911-0.0486-0.0082-0.03220.0686-0.19290.0331-0.078-0.01010.0320.077513.39144.25332.804
121.8090.44760.46091.04880.15071.0840.109-0.2092-0.42920.02170.049-0.18590.15760.0542-0.158-0.13990.0372-0.052-0.05520.06580.25711.28725.57423.371
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA29 - 1205 - 96
22AA141 - 308117 - 284
33AA309 - 341285 - 317
44AA349 - 381325 - 357
55AA384 - 431360 - 407
66AA459 - 580435 - 556
77BB29 - 1225 - 98
88BB143 - 328119 - 304
99BB329 - 340305 - 316
1010BB347 - 392323 - 368
1111BB393 - 431369 - 407
1212BB459 - 580435 - 556

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