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- PDB-3uar: Crystal structure of glutathione transferase (TARGET EFI-501774) ... -

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Basic information

Entry
Database: PDB / ID: 3uar
TitleCrystal structure of glutathione transferase (TARGET EFI-501774) from methylococcus capsulatus str. bath with gsh bound
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GSH BINDING SITE / Structural Genomics
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.6 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of Glutathione S-Transferase from Methylococcus Capsulatus
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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

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Assembly

Deposited unit
A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2753
Polymers25,8751
Non-polymers3992
Water1448
1
A: Glutathione S-transferase
hetero molecules

A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5506
Polymers51,7512
Non-polymers7994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_454-x-1/4,z+1/4,y-1/41
Buried area5080 Å2
ΔGint-27 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.932, 128.932, 128.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Glutathione S-transferase /


Mass: 25875.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: gst, MCA0074 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60CN1, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growpH: 7
Details: 0.2M SODIUM CHLORIDE, 0.1M TRIS-HCL, 30% PEG3000, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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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 7, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13203 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 11.5 % / Biso Wilson estimate: 90.817 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 11 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3UAP

3uap


Resolution: 2.6→42.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.964 / SU B: 11.395 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23718 365 3.1 %RANDOM
Rwork0.20395 ---
obs0.20498 11428 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 85.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 26 8 1641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221690
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9982295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5935206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52123.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27615281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4791512
X-RAY DIFFRACTIONr_chiral_restr0.0590.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211291
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.6321017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.65931632
X-RAY DIFFRACTIONr_scbond_it6.6894673
X-RAY DIFFRACTIONr_scangle_it9.7256661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 24 -
Rwork0.358 828 -
obs--100 %

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