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- PDB-2x64: GLUTATHIONE-S-TRANSFERASE FROM XYLELLA FASTIDIOSA -

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Basic information

Entry
Database: PDB / ID: 2x64
TitleGLUTATHIONE-S-TRANSFERASE FROM XYLELLA FASTIDIOSA
ComponentsGLUTATHIONE-S-TRANSFERASE
KeywordsTRANSFERASE / DETOXIFICATION ENZYME
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesXYLELLA FASTIDIOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMuniz, J.R.C. / Rodrigues, N.C. / Bleicher, L. / Travensolo, R.F. / Garcia, W.
CitationJournal: To be Published
Title: Structural and Biophysical Characterization of the Recombinant Glutathione-S-Transferase from Xylella
Authors: Rodrigues, N.C. / Muniz, J.R.C. / Bleicher, L. / Garcia, W. / Travensolo, R.F. / Ulian-De-Araujo, A.P. / Carrilho, E. / Garratt, R.
History
DepositionFeb 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE-S-TRANSFERASE
B: GLUTATHIONE-S-TRANSFERASE
C: GLUTATHIONE-S-TRANSFERASE
D: GLUTATHIONE-S-TRANSFERASE
E: GLUTATHIONE-S-TRANSFERASE
F: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,99118
Polymers137,9346
Non-polymers2,05712
Water13,061725
1
C: GLUTATHIONE-S-TRANSFERASE
D: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6646
Polymers45,9782
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-52.2 kcal/mol
Surface area16760 Å2
MethodPISA
2
A: GLUTATHIONE-S-TRANSFERASE
B: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6646
Polymers45,9782
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-47.4 kcal/mol
Surface area16490 Å2
MethodPISA
3
E: GLUTATHIONE-S-TRANSFERASE
F: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6646
Polymers45,9782
Non-polymers6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-50.6 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 87.890, 90.780
Angle α, β, γ (deg.)116.53, 99.33, 94.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.1816, -0.3673, 0.9122), (-0.3508, -0.8908, -0.2888), (-41.2988, -27.0163, 42.7664)
Vector: -0.9819, -31.1845, 37.1164)

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Components

#1: Protein
GLUTATHIONE-S-TRANSFERASE


Mass: 22989.076 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XYLELLA FASTIDIOSA (bacteria) / Strain: 9A5C / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9PE18
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 2.43 Å3/Da / Density % sol: 49.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→46.35 Å / Num. obs: 53809 / % possible obs: 94.5 % / Observed criterion σ(I): 1.9 / Redundancy: 2.1 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 92.1

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9091 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=GTT CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10320. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=120. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=GTT CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10320. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=120. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 2746 5.1 %RANDOM
Rwork0.1667 ---
obs0.1694 53795 --
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.9466 Å2-0.4394 Å2-0.7088 Å2
2---0.3152 Å22.2971 Å2
3---8.2617 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9553 0 126 725 10404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019950HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0613526HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3402SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes227HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1490HARMONIC5
X-RAY DIFFRACTIONt_it9950HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion18.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1234SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12066SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2825 178 4.61 %
Rwork0.2111 3680 -
all0.2145 3858 -
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)
12.65910.9568-2.07465.2752.234.77640.1329-0.44790.24780.4482-0.2040.4666-0.3819-0.31010.07110.06490.03610.0694-0.2086-0.0354-0.1821-6.2684-7.744944.9617
20.31140.1642-0.1582-0.01950.55370.7740.0504-0.10030.062-0.0081-0.04430.0796-0.4847-0.0777-0.00610.1719-0.0439-0.0255-0.16020.0294-0.08613.8056-15.237335.5641
32.1671-0.4284-0.34121.0758-1.77321.50610.12980.16070.0428-0.2359-0.0148-0.3384-0.12480.2473-0.11490.1736-0.0615-0.0483-0.16470.04350.003418.4767-16.538838.645
41.8840.59160.47983.00510.20991.85250.10990.03680.37920.1497-0.1119-0.2373-0.640.28150.00190.1978-0.067-0.0233-0.20320.0724-0.11929.0803-3.81134.9023
52.8506-1.8923-2.48394.89591.01325.69680.03030.28730.0260.1172-0.1648-0.2135-0.05060.24410.1344-0.0071-0.0178-0.0562-0.03670.0032-0.0888-0.1738-35.521327.0112
62.4213-0.31460.0322.59490.41491.97980.15380.10260.2293-0.1397-0.17060.0435-0.2125-0.26280.0168-0.0004-0.0094-0.0268-0.12010.0405-0.1129-1.4101-25.474931.1099
78.32780.08161.03871.46380.33762.99060.0118-0.07810.11660.2847-0.15170.0420.0314-0.10760.13990.1536-0.10030.0126-0.1691-0.0055-0.10776.2451-30.190151.3167
80.8167-0.011-0.35992.52570.49840.23490.05890.0238-0.17910.1518-0.11450.37670.0723-0.03510.0556-0.0239-0.03640.0154-0.0134-0.0108-0.0935-5.8789-37.363341.4291
9-1.32722.91171.59564.57540.45881.938-0.0464-0.08940.0196-0.2010.15-0.10620.20090.1737-0.10360.04310.0390.0044-0.0455-0.0309-0.1026-15.31820.4374-17.2673
100.76510.3255-0.36181.95570.13112.8742-0.0118-0.1111-0.0168-0.07690.00490.01140.21610.04830.00690.02770.0511-0.0157-0.07460.0104-0.1358-16.483-7.4384-9.82
117.3596-0.0868-0.83231.38230.49622.025-0.13460.0901-0.0379-0.31060.11580.05350.55750.21790.01880.26890.090.0786-0.12310.0205-0.1785-12.3241-24.3391-23.1483
120.5397-0.19-0.49311.2907-0.02872.8894-0.10460.18190.021-0.30120.0057-0.04330.164-0.12460.0990.0761-0.0233-0.0096-0.0566-0.0325-0.1501-22.8433-11.3739-24.519
133.86790.93321.83263.9546-2.08543.17110.08450.1832-0.3947-0.23550.00920.15910.5389-0.1415-0.0937-0.04790.0120.0143-0.15590.0248-0.1722-22.1377-27.170.9696
141.9102-1.8972-1.44412.67010.86392.9298-0.1186-0.1569-0.1624-0.0688-0.09880.08320.29060.13520.2174-0.00680.02120.0115-0.03250.0148-0.108-11.3818-16.2776-2.8375
150.84580.94231.43680.8398-1.16364.07590.1184-0.03470.0242-0.3678-0.3041-0.51490.26210.58570.1857-0.00840.17440.09380.07920.0743-0.07882.7431-19.7819-6.5043
162.0918-0.1393-0.15290.613-0.6461.6049-0.1331-0.24080.01340.1719-0.0338-0.08940.26250.33880.16680.03110.10920.00680.00530.0273-0.1348-5.4761-21.17547.2225
172.7176-1.0546-1.11936.50490.0995.63350.1812-0.08460.1666-0.2425-0.25020.3732-0.6585-0.29570.069-0.02240.1037-0.0842-0.0034-0.0795-0.1248-31.522923.15484.1911
180.8649-0.62750.23293.67521.33882.4841-0.1760.0586-0.04910.2838-0.09070.50450.3881-0.26590.26670.01660.00240.0393-0.034-0.0502-0.1072-28.783714.290415.9567
191.44391.6915-0.48427.81021.19991.98010.04930.03360.0618-0.11310.2688-0.50460.01270.332-0.3181-0.12770.0317-0.01890.0006-0.0872-0.1052-8.02522.862613.7393
201.6312-0.1324-0.082.46521.8373.1001-0.05060.03720.0495-0.10240.0347-0.01420.0760.11680.01590.00310.0529-0.0179-0.0294-0.0197-0.0688-17.480610.94285.8358
216.002-2.37871.10125.88180.89245.0928-0.0982-0.0044-0.34190.37650.1154-0.39250.89540.5648-0.01730.16680.1910.0109-0.1236-0.0469-0.274-18.945116.652937.2745
222.5282-0.8519-1.13562.8791.8033.563-0.246-0.078-0.24420.602-0.18950.39190.8843-0.08410.43550.084-0.03090.109-0.1269-0.0471-0.1529-30.287316.919527.3177
237.00471.668-1.80382.45450.9312.6079-0.0540.3020.1928-0.06360.1384-0.0895-0.221-0.0074-0.0844-0.0810.0278-0.0204-0.0713-0.0242-0.1083-19.082236.880722.5093
241.2469-1.979-0.34631.82970.6571.6732-0.0548-0.11420.12670.4983-0.13380.23450.142-0.14330.18860.0531-0.01290.0184-0.0046-0.0623-0.0691-29.607531.33934.6478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A74)
2X-RAY DIFFRACTION2(A75 - A116)
3X-RAY DIFFRACTION3(A117 - A148)
4X-RAY DIFFRACTION4(A149 - A205)
5X-RAY DIFFRACTION5(B1 - B32)
6X-RAY DIFFRACTION6(B33 - B107)
7X-RAY DIFFRACTION7(B108 - B148)
8X-RAY DIFFRACTION8(B149 - B205)
9X-RAY DIFFRACTION9(C1 - C32)
10X-RAY DIFFRACTION10(C33 - C107)
11X-RAY DIFFRACTION11(C108 - C148)
12X-RAY DIFFRACTION12(C149 - C205)
13X-RAY DIFFRACTION13(D1 - D74)
14X-RAY DIFFRACTION14(D75 - D116)
15X-RAY DIFFRACTION15(D117 - D148)
16X-RAY DIFFRACTION16(D149 - D205)
17X-RAY DIFFRACTION17(E1 - E50)
18X-RAY DIFFRACTION18(E51 - E107)
19X-RAY DIFFRACTION19(E108 - E148)
20X-RAY DIFFRACTION20(E149 - E205)
21X-RAY DIFFRACTION21(F1 - F50)
22X-RAY DIFFRACTION22(F51 - F105)
23X-RAY DIFFRACTION23(F106 - F148)
24X-RAY DIFFRACTION24(F149 - F205)

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