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- PDB-2pvq: Crystal structure of Ochrobactrum anthropi glutathione transferas... -

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Basic information

Entry
Database: PDB / ID: 2pvq
TitleCrystal structure of Ochrobactrum anthropi glutathione transferase Cys10Ala mutant with glutathione bound at the H-site
Componentsglutathione S-transferase
KeywordsTRANSFERASE / xenobiotics detoxification / glutathione / H-site
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.803 Å
AuthorsAllocati, N. / Federici, L. / Masulli, M. / Favaloro, B. / Di Ilio, C.
CitationJournal: Proteins / Year: 2008
Title: Cysteine 10 is critical for the activity of Ochrobactrum anthropi glutathione transferase and its mutation to alanine causes the preferential binding of glutathione to the H-site.
Authors: Allocati, N. / Federici, L. / Masulli, M. / Favaloro, B. / Di Ilio, C.
History
DepositionMay 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2314
Polymers21,7321
Non-polymers4993
Water3,873215
1
A: glutathione S-transferase
hetero molecules

A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4628
Polymers43,4642
Non-polymers9996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.373, 58.373, 214.023
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-86-

TYR

21A-5418-

HOH

31A-5419-

HOH

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Components

#1: Protein glutathione S-transferase / / E.C.2.5.1.18


Mass: 21731.760 Da / Num. of mol.: 1 / Mutation: C10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Gene: gst / Plasmid: pBtac1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P81065, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulfate, 100 mM Tris-HCl, 200 mM Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.803→50.64 Å / Num. all: 20967 / Num. obs: 20967 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 66.6 % / Biso Wilson estimate: 23.056 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16
Reflection shellResolution: 1.803→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.51 / Num. unique all: 2032 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
FFTmodel building
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2NTO

2nto


Resolution: 1.803→50.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.708 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.136 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24772 1074 5.1 %RANDOM
Rwork0.19762 ---
obs0.20006 19866 99.87 %-
all-20967 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20.89 Å20 Å2
2--1.77 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 1.803→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 30 215 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211597
X-RAY DIFFRACTIONr_bond_other_d0.0020.021451
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9862166
X-RAY DIFFRACTIONr_angle_other_deg0.80733378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175204
X-RAY DIFFRACTIONr_chiral_restr0.0740.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021800
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02315
X-RAY DIFFRACTIONr_nbd_refined0.2270.2393
X-RAY DIFFRACTIONr_nbd_other0.250.21651
X-RAY DIFFRACTIONr_nbtor_other0.0860.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.222
X-RAY DIFFRACTIONr_mcbond_it0.6621.51003
X-RAY DIFFRACTIONr_mcangle_it1.09321589
X-RAY DIFFRACTIONr_scbond_it1.8623594
X-RAY DIFFRACTIONr_scangle_it2.8994.5575
LS refinement shellResolution: 1.803→1.849 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 81
Rwork0.251 1413
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)
11.9949-0.3243-1.85213.87433.58245.07220.00690.0380.01180.02490.0401-0.23770.12360.2915-0.0470.09450.013-0.03820.1218-0.01330.11648.035414.343456.2189
23.7891.5853-0.25165.7433-0.54553.2960.16580.0250.0217-0.0026-0.12060.05130.15440.2768-0.04520.02740.037-0.01050.0847-0.03120.06344.95818.437248.8094
30.91940.04220.45191.2265-1.23642.1319-0.0032-0.049-0.07420.092-0.0187-0.11590.04110.07330.02190.11520.0043-0.01550.1556-0.00570.153350.257512.620559.9078
43.1827-2.8936-2.20692.4395-3.3099-1.4902-0.0413-0.43160.00930.1910.08740.17380.11960.1731-0.04610.12-0.0227-0.04790.1235-0.01140.145745.241710.130267.7202
52.2304-0.09151.10190.96750.29922.9057-0.0267-0.09750.00240.0115-0.02980.0655-0.08870.12750.05650.0542-0.0052-0.03320.07210.00640.082641.07217.734162.8484
63.14453.89260.33238.5137-0.20215.16370.0304-0.03980.04710.1591-0.0051-0.1604-0.04040.1086-0.02540.0015-0.0004-0.00640.076-0.03290.044437.814423.172154.0384
75.58450.1127-4.81862.2149-0.33145.02930.11740.14030.3970.0147-0.15660.0265-0.0497-0.10390.03920.05980.00820.01020.051-0.00680.073635.727430.329147.0607
82.0818-1.82720.11535.1428-0.00610.94360.05110.0995-0.0472-0.0357-0.0498-0.06450.09640.0339-0.00130.0547-0.01070.0010.0935-0.01330.056231.040613.610346.9326
91.0732-0.33670.48732.2355-1.60472.0823-0.0442-0.0802-0.05970.09190.11320.00250.0448-0.0187-0.0690.12280.00490.00110.1013-0.03820.096831.7499-0.083843.0215
100.63580.43730.82360.9115-1.27574.7103-0.02070.31540.0099-0.14120.03310.1678-0.09140.1555-0.01250.08220.01950.01570.0781-0.00880.091533.81721.750135.8896
111.0867-1.9829-0.25528.50280.4343-0.180.20050.1298-0.2109-0.1529-0.28440.16490.1440.03110.08390.08150.0131-0.02560.1098-0.02270.096839.864810.164543.3629
120.5574-2.571-1.17524.9283-1.51162.3114-0.3187-0.33070.00440.1270.224-0.2237-0.2023-0.13450.09470.12570.041-0.00010.1192-0.03960.12138.30880.814235.0834
130.28440.2742-0.29150.21930.0155-0.70060.0240.1454-0.1431-0.00040.0173-0.15080.13070.2572-0.04130.14530.02750.01110.1674-0.02760.138846.117915.044438.7267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION2AA10 - 2010 - 20
3X-RAY DIFFRACTION3AA21 - 4021 - 40
4X-RAY DIFFRACTION4AA41 - 4641 - 46
5X-RAY DIFFRACTION5AA47 - 6547 - 65
6X-RAY DIFFRACTION6AA66 - 7666 - 76
7X-RAY DIFFRACTION7AA77 - 8777 - 87
8X-RAY DIFFRACTION8AA88 - 11388 - 113
9X-RAY DIFFRACTION9AA114 - 140114 - 140
10X-RAY DIFFRACTION10AA141 - 152141 - 152
11X-RAY DIFFRACTION11AA153 - 168153 - 168
12X-RAY DIFFRACTION12AA169 - 175169 - 175
13X-RAY DIFFRACTION13AA176 - 201176 - 201

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