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- PDB-5hwi: Crystal structure of selenomethionine labelled gama glutamyl cycl... -

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Basic information

Entry
Database: PDB / ID: 5hwi
TitleCrystal structure of selenomethionine labelled 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
SUCCINIC ACID / Glutathione-specific gamma-glutamylcyclotransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.755 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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9843
Polymers27,7741
Non-polymers2102
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint4 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)110.545, 110.545, 42.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-494-

HOH

21A-541-

HOH

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Components

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


Mass: 27773.613 Da / Num. of mol.: 1 / Mutation: S42M,L77M,A141M,V176M
Source method: isolated from a genetically manipulated source
Details: Mutated original sequence to Methionine for generating Se-Met protein
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GCG1 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P32656, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 51 % / Description: Rectangular Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M Succinic acid, 0.1 M HEPES, 1%(w/v) PEG MME-2000
PH range: 6.8 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787 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: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25966 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 34.9 % / Biso Wilson estimate: 26.84 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.1 / Net I/σ(I): 41.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.83 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: SAD / Resolution: 1.755→37.4 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 1163 4.83 %Random Selection
Rwork0.1677 ---
obs0.1697 24069 95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.755→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 14 142 1948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151902
X-RAY DIFFRACTIONf_angle_d1.2122602
X-RAY DIFFRACTIONf_dihedral_angle_d2.7761525
X-RAY DIFFRACTIONf_chiral_restr0.087289
X-RAY DIFFRACTIONf_plane_restr0.009339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.755-1.79080.27841090.25572069X-RAY DIFFRACTION73
1.7908-1.82970.28281060.23882267X-RAY DIFFRACTION80
1.8297-1.87230.25361260.22092452X-RAY DIFFRACTION87
1.8723-1.91910.25551280.19952593X-RAY DIFFRACTION92
1.9191-1.9710.24771480.19052734X-RAY DIFFRACTION97
1.971-2.0290.21991380.17722837X-RAY DIFFRACTION100
2.029-2.09450.23681410.17392781X-RAY DIFFRACTION99
2.0945-2.16930.23051560.17432777X-RAY DIFFRACTION99
2.1693-2.25620.17781310.15952834X-RAY DIFFRACTION99
2.2562-2.35880.21731360.17312793X-RAY DIFFRACTION99
2.3588-2.48320.21661480.17372794X-RAY DIFFRACTION99
2.4832-2.63870.24151280.18622834X-RAY DIFFRACTION99
2.6387-2.84240.21191430.16642820X-RAY DIFFRACTION99
2.8424-3.12830.21741560.16332778X-RAY DIFFRACTION100
3.1283-3.58060.18681470.14632810X-RAY DIFFRACTION100
3.5806-4.510.1821320.13552821X-RAY DIFFRACTION100
4.51-37.40880.20461530.18082817X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.1313 Å / Origin y: 57.3614 Å / Origin z: 16.9669 Å
111213212223313233
T0.134 Å2-0.0271 Å2-0.0128 Å2-0.1639 Å20.0009 Å2--0.164 Å2
L2.4561 °2-1.9018 °20.4459 °2-3.5416 °2-0.5341 °2--1.3145 °2
S0.0048 Å °0.1355 Å °0.0286 Å °-0.0544 Å °-0.0598 Å °-0.1026 Å °-0.0295 Å °0.0977 Å °0.0331 Å °
Refinement TLS groupSelection details: all

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