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- PDB-6ky0: Crystal structural of active-site human glutathione-specific gamm... -

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Basic information

Entry
Database: PDB / ID: 6ky0
TitleCrystal structural of active-site human glutathione-specific gamma-glutamylcyclotransferase 2(ChaC2) mutant with Glutamate 74 replaced by Glutamine
ComponentsGlutathione-specific gamma-glutamylcyclotransferase 2
KeywordsTRANSFERASE / gamma-glutamylcyclotransferase / ChaC2 / GSH degradation / active-site mutant
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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.06 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: To Be Published
Title: Glutathione specific gamma-glutamylcyclotransferase 2 mutant with Glutamate 74 replaced by Glutamine
Authors: Nguyen, T.K.Y. / Han, B.W.
History
DepositionSep 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 2
B: Glutathione-specific gamma-glutamylcyclotransferase 2
C: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)61,3413
Polymers61,3413
Non-polymers00
Water1,27971
1
A: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,4471
Polymers20,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,4471
Polymers20,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,4471
Polymers20,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.996, 72.996, 104.324
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 20447.146 Da / Num. of mol.: 3 / Mutation: E74Q, 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.: 71 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3M sodium acetate trihydrate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 38639 / % possible obs: 99.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 22.7
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 1956 / Rsym value: 0.826

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Processing

Software
NameVersionClassification
REFMACrefmac 5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K95

6k95


Resolution: 2.06→31.63 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.146 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.184
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1996 5.2 %RANDOM
Rwork0.2253 ---
obs0.2253 36500 98.79 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 141.66 Å2 / Biso mean: 36.14 Å2 / Biso min: 29.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.7 Å20 Å2
2--1.39 Å20 Å2
3----4.51 Å2
Refinement stepCycle: final / Resolution: 2.06→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 0 71 4212
Biso mean---50.81 -
Num. residues----518
LS refinement shellResolution: 2.06→2.108 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.298 148 -
Rwork0.287 2698 -
obs--98.79 %
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)
13.2005-1.20731.48621.221-0.24134.3515-0.1087-0.0147-0.04220.11770.0377-0.0133-0.1025-0.38720.0710.11410.0280.01650.0658-0.01360.00983.409-5.66111.191
22.2974-1.2060.84591.4799-1.11734.5502-0.02440.1387-0.0023-0.006-0.02580.02120.28620.22390.05020.0486-0.01260.01410.1086-0.00910.005429.959-20.933-12.651
30.97371.39041.78162.91282.14924.9754-0.0344-0.064-0.0153-0.10120.0271-0.0347-0.31560.33220.00730.429-0.0240.00030.47060.00320.390238.16716.4271.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 174
2X-RAY DIFFRACTION2B-6 - 174
3X-RAY DIFFRACTION3C0 - 174

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