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- PDB-4nhw: Crystal structure of glutathione transferase SMc00097 from Sinorh... -

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Basic information

Entry
Database: PDB / ID: 4nhw
TitleCrystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275, with one glutathione bound per one protein subunit
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / glutathione S-transferase / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione transferase SMc00097 from Sinorhizobium meliloti, target EFI-507275
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 20, 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9368
Polymers107,7064
Non-polymers1,2294
Water4,125229
1
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4684
Polymers53,8532
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-29 kcal/mol
Surface area19200 Å2
MethodPISA
2
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4684
Polymers53,8532
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-26 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.306, 62.504, 84.426
Angle α, β, γ (deg.)87.34, 79.73, 82.04
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.229874, 0.646171, -0.72775), (0.646875, -0.660134, -0.381806), (-0.727125, -0.382996, -0.56974)59.36735, -59.805, 47.45424
3given(0.999235, -0.028986, -0.02625), (-0.022264, -0.973528, 0.227481), (-0.032149, -0.226723, -0.973429)-15.76049, -7.91959, -6.53729
4given(0.220486, -0.475838, 0.851448), (0.668718, 0.709227, 0.223189), (-0.710072, 0.520169, 0.474577)57.40273, -62.13658, 67.04572

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Components

#1: Protein
Glutathione S-transferase


Mass: 26926.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: gst2, SM2011_c00097 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M4MQ92, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growpH: 6.5
Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, vapor diffusion, ...Details: Protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 25% PEG3350, 0.1M bis-tris pH 6.5, 0.2M ammonium acetate, 5 mM GSH, cryoprotectant: none, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 62866 / % possible obs: 96.1 % / Observed criterion σ(I): -5 / Redundancy: 2 % / Rsym value: 0.047 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.1 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LSZ

3lsz


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.136 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22553 1906 3 %RANDOM
Rwork0.1728 ---
obs0.17437 60645 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0.59 Å2-2.71 Å2
2---0.23 Å2-0.2 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 80 229 7021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196980
X-RAY DIFFRACTIONr_bond_other_d0.0010.026707
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9739480
X-RAY DIFFRACTIONr_angle_other_deg0.743315374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6822.866314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.037151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8341565
X-RAY DIFFRACTIONr_chiral_restr0.0620.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021624
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.5235.3253434
X-RAY DIFFRACTIONr_mcbond_other9.5115.3243433
X-RAY DIFFRACTIONr_mcangle_it10.9148.9224280
X-RAY DIFFRACTIONr_mcangle_other10.9158.9244281
X-RAY DIFFRACTIONr_scbond_it12.1755.9253546
X-RAY DIFFRACTIONr_scbond_other12.175.9253546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.2449.6655198
X-RAY DIFFRACTIONr_long_range_B_refined13.73824.1688017
X-RAY DIFFRACTIONr_long_range_B_other13.73924.1718018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 122 -
Rwork0.349 4006 -
obs--86.36 %
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)
12.8157-0.54571.53352.7209-0.43594.2872-0.0219-0.0792-0.4620.31810.02880.28890.6987-0.1705-0.00680.1972-0.01430.07810.0251-0.00120.1118111.72260.1661-25.7757
23.6763-0.44531.56411.2082-0.20683.6342-0.0869-0.21470.26840.32740.03010.31710.0108-0.42540.05690.09440.0020.07890.051-0.0130.1477103.825322.2249-19.1713
31.95580.27-0.87342.1812-0.67214.10540.04640.10680.2675-0.0983-0.09850.0625-0.5176-0.12230.05210.1773-0.0064-0.05140.02420.01760.0555127.8172-7.172117.1329
42.39860.6278-0.54691.7528-0.26793.44750.0887-0.0106-0.2749-0.1292-0.0860.16150.0745-0.2987-0.00260.0375-0.0009-0.050.0352-0.00030.0954120.1705-30.370717.4998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 219
2X-RAY DIFFRACTION2B1 - 219
3X-RAY DIFFRACTION3C1 - 219
4X-RAY DIFFRACTION4D-7 - 219

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