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- PDB-6ky1: Crystal structural of human glutathione-specific gamma-glutamylcy... -

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Basic information

Entry
Database: PDB / ID: 6ky1
TitleCrystal structural of human glutathione-specific gamma-glutamylcyclotransferase 2 (ChaC2)mutant with Glutamate 83 replaced by Glutamine
ComponentsGlutathione-specific gamma-glutamylcyclotransferase 2
KeywordsTRANSFERASE / gamma-glutamylcyclotransferase / ChaC2 / GSH degradation / Domain Swapping.
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: 2.04 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 83 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

Downloads & links

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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)61,6813
Polymers61,6813
Non-polymers00
Water1,53185
1
A: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,5601
Polymers20,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,5601
Polymers20,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione-specific gamma-glutamylcyclotransferase 2


Theoretical massNumber of molelcules
Total (without water)20,5601
Polymers20,5601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.707, 72.707, 103.998
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: 20560.305 Da / Num. of mol.: 3 / Mutation: R82G, E83Q
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.: 85 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3 M 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: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 36804 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rsym value: 0.07 / Net I/σ(I): 42.521
Reflection shellResolution: 2.04→2.08 Å / Rsym value: 0.563

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K95

6k95


Resolution: 2.04→31.48 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.58 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.038
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 2062 5.3 %RANDOM
Rwork0.2254 ---
obs0.2269 36804 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.19 Å2 / Biso mean: 59.567 Å2 / Biso min: 30.83 Å2
Baniso -1Baniso -2Baniso -3
1-18.76 Å2-0 Å20 Å2
2--18.76 Å20 Å2
3----37.53 Å2
Refinement stepCycle: final / Resolution: 2.04→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 0 85 4185
Biso mean---60.26 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173851
X-RAY DIFFRACTIONr_angle_refined_deg1.331.6555738
X-RAY DIFFRACTIONr_angle_other_deg1.1621.5768917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.3521.454227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44715646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6571529
X-RAY DIFFRACTIONr_chiral_restr0.060.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02958
LS refinement shellResolution: 2.042→2.095 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 204 -
Rwork0.47 2558 -
all-2762 -
obs--95.7 %
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)
12.66271.1183-1.01631.3189-1.00783.6604-0.0633-0.07740.0652-0.0125-0.03260.048-0.22970.210.09590.11220.0118-0.02980.1607-0.00820.01929.759-20.95-0.092
22.7361.0992-1.21621.5045-0.12484.265-0.06450.02350.0645-0.08090.02750.0127-0.0312-0.29340.0370.128-0.0009-0.02020.0826-0.0180.00883.21-36.328-23.72
32.066-1.45391.49993.089-2.63074.9407-0.0275-0.0890.03210.11450.02890.09390.29170.1281-0.00140.46140.00180.02220.45610.00660.263730.948-60.674-9.01
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 174
2X-RAY DIFFRACTION2B-5 - 174
3X-RAY DIFFRACTION3C0 - 174

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