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- PDB-6k95: Crystal structural of human glutathione-specific gamma-glutamylcy... -

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Basic information

Entry
Database: PDB / ID: 6k95
TitleCrystal structural of human glutathione-specific gamma-glutamylcyclotransferase 2 (ChaC2)
ComponentsGlutathione-specific gamma-glutamylcyclotransferase 2
KeywordsTRANSFERASE / gamma-glutamylcyclotransferase / ChaC2 / GSH degradation / swapped-domain dimer
Function / homology
Function and homology information


glutathione-specific gamma-glutamylcyclotransferase / glutathione specific gamma-glutamylcyclotransferase activity / gamma-glutamylcyclotransferase activity / Glutathione synthesis and recycling / glutathione catabolic process / glutathione biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Glutathione-specific gamma-glutamylcyclotransferase / ChaC-like protein / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily
Similarity search - Domain/homology
Glutathione-specific gamma-glutamylcyclotransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å
AuthorsNguyen, T.K.Y. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2011-0030001 Korea, Republic Of
CitationJournal: Biomolecules / Year: 2019
Title: Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism.
Authors: Nguyen, Y.T.K. / Park, J.S. / Jang, J.Y. / Kim, K.R. / Vo, T.T.L. / Kim, K.W. / Han, B.W.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 2
B: Glutathione-specific gamma-glutamylcyclotransferase 2
C: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)62,3933
Polymers62,3933
Non-polymers00
Water19811
1
A: Glutathione-specific gamma-glutamylcyclotransferase 2

A: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)41,5952
Polymers41,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
MethodPISA
2
B: Glutathione-specific gamma-glutamylcyclotransferase 2

C: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)41,5952
Polymers41,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2510 Å2
ΔGint-9 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.842, 62.161, 103.625
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutathione-specific gamma-glutamylcyclotransferase 2 / Gamma-GCG 2 / Cation transport regulator-like protein 2


Mass: 20797.529 Da / Num. of mol.: 3 / Mutation: R82G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHAC2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WUX2, glutathione-specific gamma-glutamylcyclotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14%(w/v) polyethylene-glycol 8,000 (PEG 8000), 14% PEG, 100mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.288→50 Å / Num. obs: 31131 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rsym value: 0.056 / Net I/σ(I): 23.006
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.2 % / Rsym value: 0.403

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.29→37.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / SU B: 28.847 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.236
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1554 5 %RANDOM
Rwork0.2391 ---
obs0.2405 29645 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 137.9 Å2 / Biso mean: 47.36 Å2 / Biso min: 51.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0 Å20.3 Å2
2--1.73 Å20 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 2.29→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 0 11 4187
Biso mean---71.26 -
Num. residues----522
Refine LS restraintsType: r_xyhbond_nbd_refined
LS refinement shellResolution: 2.29→2.347 Å / Num. reflection Rfree: 109 / Rfactor Rfree error: 0
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)
14.52920.7771-2.15790.53340.72034.48460.14930.36720.07630.0859-0.0625-0.0214-0.3234-0.3905-0.08680.51420.0707-0.05610.30890.01220.0139.813-6.89141.673
20.87930.6721.33723.15091.32873.9954-0.20920.0178-0.1014-0.13710.2337-0.0212-0.06840.5543-0.02450.2997-0.01240.0390.39390.03370.020738.031-15.6667.048
31.82491.4674-0.16522.01841.834.80610.1661-0.0439-0.04240.2738-0.0589-0.09640.43190.1714-0.10720.4750.1145-0.01690.24140.0450.014723.10921.16427.479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 177
2X-RAY DIFFRACTION2B2 - 175
3X-RAY DIFFRACTION3C1 - 176

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