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- PDB-5hwk: Crystal structure of gama glutamyl cyclotransferease specific to ... -

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Basic information

Entry
Database: PDB / ID: 5hwk
TitleCrystal structure of gama glutamyl cyclotransferease specific to glutathione from yeast
ComponentsGlutathione-specific gamma-glutamylcyclotransferase
KeywordsTRANSFERASE / ChaC / GCG1 / Yer163c / glutathione / oxo-proline
Function / homology
Function and homology information


glutathione-specific gamma-glutamylcyclotransferase / Glutathione synthesis and recycling / glutathione specific gamma-glutamylcyclotransferase activity / gamma-glutamylcyclotransferase activity / glutathione catabolic process / nucleus / cytoplasm
Similarity search - Function
Glutathione-specific gamma-glutamylcyclotransferase / ChaC-like protein / Gamma-glutamyl cyclotransferase-like
Similarity search - Domain/homology
BENZOIC ACID / PHOSPHATE ION / Glutathione-specific gamma-glutamylcyclotransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.344 Å
AuthorsKaur, A. / Gautam, R. / Srivastava, R. / Chandel, A. / Kumar, A. / Karthikeyan, S. / Bachhawat, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and TechnologySB/SO/BB/017/2014 India
CitationJournal: J. Biol. Chem. / Year: 2017
Title: ChaC2, an Enzyme for Slow Turnover of Cytosolic Glutathione
Authors: Kaur, A. / Gautam, R. / Srivastava, R. / Chandel, A. / Kumar, A. / Karthikeyan, S. / Bachhawat, A.K.
History
DepositionJan 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione-specific gamma-glutamylcyclotransferase
B: Glutathione-specific gamma-glutamylcyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2986
Polymers54,8632
Non-polymers4344
Water7,945441
1
A: Glutathione-specific gamma-glutamylcyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6493
Polymers27,4321
Non-polymers2172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10330 Å2
MethodPISA
2
B: Glutathione-specific gamma-glutamylcyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6493
Polymers27,4321
Non-polymers2172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-9 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.779, 62.019, 61.695
Angle α, β, γ (deg.)113.71, 89.89, 101.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glutathione-specific gamma-glutamylcyclotransferase / Gamma-GCG


Mass: 27431.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GCG1 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P32656, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium Phosphate, 20% PEG3350, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014 / Details: MIRROR
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 103046 / % possible obs: 84.5 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / CC1/2: 0.83 / % possible all: 32.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HWI

5hwi


Resolution: 1.344→30.143 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 5039 4.89 %
Rwork0.1607 --
obs0.1624 103007 83.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.344→30.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 28 441 3919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123654
X-RAY DIFFRACTIONf_angle_d1.1835019
X-RAY DIFFRACTIONf_dihedral_angle_d6.6282405
X-RAY DIFFRACTIONf_chiral_restr0.096566
X-RAY DIFFRACTIONf_plane_restr0.009657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3443-1.35960.2759400.2405833X-RAY DIFFRACTION22
1.3596-1.37560.2868570.21121199X-RAY DIFFRACTION31
1.3756-1.39240.2638690.20641416X-RAY DIFFRACTION36
1.3924-1.410.268850.20091685X-RAY DIFFRACTION43
1.41-1.42850.2324890.19741956X-RAY DIFFRACTION50
1.4285-1.44810.21721250.1892334X-RAY DIFFRACTION60
1.4481-1.46880.24861320.17342796X-RAY DIFFRACTION71
1.4688-1.49070.22441630.17193463X-RAY DIFFRACTION88
1.4907-1.5140.22161970.15563646X-RAY DIFFRACTION94
1.514-1.53880.19091940.1493670X-RAY DIFFRACTION94
1.5388-1.56540.17671900.14243694X-RAY DIFFRACTION95
1.5654-1.59380.20611900.13853716X-RAY DIFFRACTION95
1.5938-1.62450.18271860.13473719X-RAY DIFFRACTION95
1.6245-1.65760.1891900.13523700X-RAY DIFFRACTION95
1.6576-1.69370.15961990.13133730X-RAY DIFFRACTION96
1.6937-1.73310.18822190.13723758X-RAY DIFFRACTION96
1.7331-1.77640.1922100.14093660X-RAY DIFFRACTION96
1.7764-1.82440.17392150.13933744X-RAY DIFFRACTION96
1.8244-1.87810.19131820.14323748X-RAY DIFFRACTION96
1.8781-1.93870.18121810.14373757X-RAY DIFFRACTION96
1.9387-2.0080.17132080.14033743X-RAY DIFFRACTION97
2.008-2.08840.18461700.15043810X-RAY DIFFRACTION97
2.0884-2.18340.1991760.15593813X-RAY DIFFRACTION97
2.1834-2.29850.20521810.15693777X-RAY DIFFRACTION97
2.2985-2.44240.19581920.15963824X-RAY DIFFRACTION98
2.4424-2.63090.1882140.17273790X-RAY DIFFRACTION98
2.6309-2.89550.21621930.17813839X-RAY DIFFRACTION98
2.8955-3.3140.2192220.17713806X-RAY DIFFRACTION99
3.314-4.17350.16171960.1523878X-RAY DIFFRACTION99
4.1735-30.15070.19871740.17263464X-RAY DIFFRACTION89

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