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- PDB-4dej: Crystal structure of glutathione transferase-like protein IL0419 ... -

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Basic information

Entry
Database: PDB / ID: 4dej
TitleCrystal structure of glutathione transferase-like protein IL0419 (Target EFI-501089) from Idiomarina loihiensis L2TR
ComponentsGlutathione S-transferase related protein
KeywordsTRANSFERASE / TRANSFERASE-LIKE PROTEIN / TRANSCRIPTION REGULATION / Structural Genomics
Function / homology
Function and homology information


transferase activity / cytoplasm
Similarity search - Function
Stringent starvation protein A, C-terminal / : / 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. ...Stringent starvation protein A, C-terminal / : / 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 related protein
Similarity search - Component
Biological speciesIdiomarina loihiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.9 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-Like Protein Il0419 from Idiomarina Loihiensis
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
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase related protein
B: Glutathione S-transferase related protein
C: Glutathione S-transferase related protein
D: Glutathione S-transferase related protein
E: Glutathione S-transferase related protein
F: Glutathione S-transferase related protein
G: Glutathione S-transferase related protein
H: Glutathione S-transferase related protein
I: Glutathione S-transferase related protein
J: Glutathione S-transferase related protein
K: Glutathione S-transferase related protein
L: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)324,13012
Polymers324,13012
Non-polymers00
Water25214
1
A: Glutathione S-transferase related protein
B: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-11 kcal/mol
Surface area20220 Å2
MethodPISA
2
C: Glutathione S-transferase related protein
D: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-10 kcal/mol
Surface area20320 Å2
MethodPISA
3
E: Glutathione S-transferase related protein
F: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-10 kcal/mol
Surface area19670 Å2
MethodPISA
4
G: Glutathione S-transferase related protein
H: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area20210 Å2
MethodPISA
5
I: Glutathione S-transferase related protein
J: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-9 kcal/mol
Surface area20210 Å2
MethodPISA
6
K: Glutathione S-transferase related protein
L: Glutathione S-transferase related protein


Theoretical massNumber of molelcules
Total (without water)54,0222
Polymers54,0222
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.356, 156.988, 244.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.06297, -0.993066, 0.099274), (-0.993908, -0.071415, -0.083949), (0.090456, -0.093383, -0.991513)28.14882, 24.21758, -60.4441
3given(-0.505955, -0.862185, -0.025431), (0.859052, -0.506335, 0.075194), (-0.077708, 0.016199, 0.996845)38.90466, -18.10287, 1.32895
4given(-0.894655, 0.446576, 0.012707), (0.445352, 0.893735, -0.053838), (-0.0354, -0.042508, -0.998469)48.28802, -12.88725, -56.69899
5given(0.031073, -0.979798, -0.197563), (0.991836, 0.005768, 0.127392), (-0.123678, -0.199908, 0.971978)29.67529, -36.48215, -57.77267
6given(-0.993948, -0.090377, -0.062442), (-0.096359, 0.990253, 0.100564), (0.052745, 0.105973, -0.992969)60.7355, 2.51411, 2.2404
7given(0.834023, 0.550027, 0.043309), (0.551135, -0.834197, -0.019111), (0.025617, 0.039808, -0.998879)4.67493, -12.32195, -58.51945
8given(-0.497635, 0.865428, -0.05825), (-0.867384, -0.496654, 0.031283), (-0.001857, 0.066093, 0.997812)35.56178, 25.10925, -0.40379
9given(0.405938, 0.887853, 0.216637), (0.912072, -0.408567, -0.034609), (0.057783, 0.211638, -0.975639)6.20095, -28.72876, 1.01417
10given(-0.873555, 0.483569, -0.055334), (-0.475164, -0.871908, -0.118302), (-0.105454, -0.077051, 0.991435)57.31174, 19.71381, -58.61235
11given(0.844687, 0.523661, 0.11083), (-0.534516, 0.836153, 0.123049), (-0.028235, -0.163179, 0.986192)-5.71096, 16.37544, -60.77655
12given(-0.873555, 0.483569, -0.055334), (-0.475164, -0.871908, -0.118302), (-0.105454, -0.077051, 0.991435)57.31174, 19.71381, -58.61235

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Components

#1: Protein
Glutathione S-transferase related protein


Mass: 27010.842 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Strain: ATCC BAA-735 / DSM 15497 / L2-TR / Gene: sspA, IL0419 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5R0K1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M AMMONIUM SULFATE, 0.1M HEPES-NA, 30% PEG8000', pH 7.5, 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: Aug 9, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→70 Å / Num. obs: 87401 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 6.7 % / Biso Wilson estimate: 96.503 Å2 / Rsym value: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.7 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 1YY7

1yy7


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.436 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27533 2361 3 %RANDOM
Rwork0.20743 ---
obs0.20951 76132 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 104.323 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19577 0 0 14 19591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0220013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.99627136
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25852397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17424.223959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.426153597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.70615145
X-RAY DIFFRACTIONr_chiral_restr0.0720.22986
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115177
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 159 -
Rwork0.346 5182 -
obs--99.13 %

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