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- PDB-2nto: Structure of the Glutathione Transferase from Ochrobactrum anthro... -

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Basic information

Entry
Database: PDB / ID: 2nto
TitleStructure of the Glutathione Transferase from Ochrobactrum anthropi in complex with glutathione
Componentsglutathione S-transferase
KeywordsTRANSFERASE / N-terminal alpha+beta domain / C-terminal all helical domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsFederici, L. / Bonivento, D. / Di Matteo, A. / Allocati, N.
CitationJournal: Biochem.J. / Year: 2007
Title: Role of Ser11 in the stabilization of the structure of Ochrobactrum anthropi glutathione transferase
Authors: Federici, L. / Masulli, M. / Bonivento, D. / Di Matteo, A. / Gianni, S. / Favaloro, B. / Di Ilio, C. / Allocati, N.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Non-polymer description
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1673
Polymers21,7641
Non-polymers4032
Water2,216123
1
A: glutathione S-transferase
hetero molecules

A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3346
Polymers43,5282
Non-polymers8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)58.765, 58.765, 212.323
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-213-

HOH

DetailsThe second part of the biological assembly is generated by applying the following matrix. Ration: -1 0 0 0 1 0 0 0 -1 translation: 58.7833 0 106.151

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Components

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


Mass: 21763.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Gene: gst / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P81065, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 49.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M Ammonium Sulphate, 0.1 M Tris pH 7.0, 0.2 M lithium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2005
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: 2.095→50.64 Å / Num. all: 13632 / Num. obs: 13632 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 13.2 % / Biso Wilson estimate: 26.251 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.095→2.18 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 8.41 / Num. unique all: 1312 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0F

1a0f


Resolution: 2.095→50.64 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.295 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.211 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23181 676 5 %RANDOM
Rwork0.18744 ---
all0.18955 13632 --
obs0.18955 12924 99.79 %-
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: 15.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.48 Å20 Å2
2--0.97 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.095→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 25 123 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211604
X-RAY DIFFRACTIONr_bond_other_d0.0020.021461
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9842174
X-RAY DIFFRACTIONr_angle_other_deg0.84133399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2625202
X-RAY DIFFRACTIONr_chiral_restr0.1070.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021808
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02319
X-RAY DIFFRACTIONr_nbd_refined0.2210.2386
X-RAY DIFFRACTIONr_nbd_other0.2480.21624
X-RAY DIFFRACTIONr_nbtor_other0.0860.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.215
X-RAY DIFFRACTIONr_mcbond_it0.5751.51004
X-RAY DIFFRACTIONr_mcangle_it1.09421592
X-RAY DIFFRACTIONr_scbond_it1.6923600
X-RAY DIFFRACTIONr_scangle_it2.7654.5582
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 44
Rwork0.23 898
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)
12.2007-0.1321-2.1816.02795.18237.0310.08790.13480.02060.09730.0598-0.13170.08610.3764-0.14770.01490.0256-0.00660.1235-0.02420.09247.649513.874255.438
20.8532-1.51640.97414.123-3.20264.03260.03180.10720.06250.10550.0197-0.2084-0.210.1797-0.05140.0216-0.01010.00190.1403-0.04040.108447.833619.662451.526
37.1663-0.2887-1.13571.3641-1.50043.02090.1565-0.1755-0.32130.0672-0.1479-0.11650.11370.0292-0.00860.07280.0079-0.0720.0745-0.00470.117545.84768.016964.3589
42.28553.41942.07934.86022.47129.2082-0.1138-0.08780.018-0.0583-0.00430.0678-0.31650.15930.11820.05450.0031-0.05110.0971-0.0070.090342.64521.325562.5382
51.01921.0236-0.26255.0837-1.79151.23970.05180.0256-0.07730.0877-0.04-0.049-0.04550.1555-0.01170.0756-0.0122-0.00030.1158-0.01910.088837.706822.365353.9594
62.5484-0.0175-3.1991.69511.43215.09620.06430.22950.11470.0393-0.05270.0163-0.1837-0.1678-0.01150.1022-0.02290.02750.0875-0.00090.064235.201430.336946.764
70.0386-0.431-0.27943.31770.6930.6526-0.0095-0.00060.0290.11090.1002-0.14690.1101-0.0028-0.09060.0891-0.0029-0.01950.0966-0.01670.092931.2496.275344.9157
80.53990.24431.28720.5553-1.95938.6368-0.06930.14350.0527-0.09250.18550.1639-0.02030.0179-0.11620.0788-0.01330.00410.0961-0.00050.080933.625921.123634.7178
9-0.88090.7577-0.06932.87951.44781.59850.0110.0740.00520.00420.0069-0.19780.08670.1132-0.01780.08430.02390.00440.1293-0.04660.10339.56017.74340.854
101.29260.71711.72140.85770.09311.852500.3449-0.2016-0.29460.1146-0.26570.10110.4344-0.11460.05230.01340.05750.1969-0.05390.087645.689314.286338.1971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 101 - 10
2X-RAY DIFFRACTION2AA11 - 3011 - 30
3X-RAY DIFFRACTION3AA31 - 5231 - 52
4X-RAY DIFFRACTION4AA53 - 6453 - 64
5X-RAY DIFFRACTION5AA65 - 7665 - 76
6X-RAY DIFFRACTION6AA77 - 8777 - 87
7X-RAY DIFFRACTION7AA88 - 13988 - 139
8X-RAY DIFFRACTION8AA140 - 151140 - 151
9X-RAY DIFFRACTION9AA152 - 174152 - 174
10X-RAY DIFFRACTION10AA175 - 201175 - 201

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