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- PDB-4hz4: Crystal structure of glutathione s-transferase b4xh91 (target efi... -

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Basic information

Entry
Database: PDB / ID: 4hz4
TitleCrystal structure of glutathione s-transferase b4xh91 (target efi-501787) from actinobacillus pleuropneumoniae
ComponentsGlutathione-S-transferase
KeywordsTRANSFERASE / GLUTATHIONE / ENZYME FUNCTION INITIATIVE / Structural Genomics
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-S-transferase
Similarity search - Component
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N.F. / 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 s-transferase b4xh91 from Actinobacillus pleuropneumoniae
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Al Obaidi, N.F. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6922
Polymers24,6001
Non-polymers921
Water3,369187
1
A: Glutathione-S-transferase
hetero molecules

A: Glutathione-S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3844
Polymers49,2002
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4730 Å2
ΔGint-22 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.406, 54.406, 150.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

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Components

#1: Protein Glutathione-S-transferase


Mass: 24599.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Strain: 56153 / Gene: appser11_13220, gst / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4XH91
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M SODIUM HYDROGEN PHOSPHATE:CITRIC ACID, PH 4.2, 1.6M SODIUM DIHYDROGEN PHOSPHATE, 0.4M POTASSIUM HYDROGEN PHOSPHATE , VAPOR DIFFUSION, SITTING DROP

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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 26, 2012 / 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: 1.62→50 Å / Num. obs: 29710 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 25.4 % / Biso Wilson estimate: 23.157 Å2 / Rsym value: 0.063 / Net I/σ(I): 12.9
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 25.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UAP

3uap


Resolution: 1.62→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.768 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18719 952 3.2 %RANDOM
Rwork0.13973 ---
obs0.14114 28713 99.85 %-
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: 29.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 6 187 1908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9572444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9755225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79124.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.756155
X-RAY DIFFRACTIONr_chiral_restr0.0720.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211390
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_it4.5321088
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.40731739
X-RAY DIFFRACTIONr_scbond_it7.8333705
X-RAY DIFFRACTIONr_scangle_it10.755701
X-RAY DIFFRACTIONr_rigid_bond_restr4.57931793
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.621→1.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 74 -
Rwork0.128 2061 -
obs--100 %

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