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- PDB-3lq7: Crystal structure of glutathione s-transferase from agrobacterium... -

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Basic information

Entry
Database: PDB / ID: 3lq7
TitleCrystal structure of glutathione s-transferase from agrobacterium tumefaciens str. c58
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 S-transferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Toro, R. / Gilmore, M. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Glutathione S-Transferase from Agrobacterium Tumefaciens
Authors: Patskovsky, Y. / Toro, R. / Gilmore, M. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)82,1653
Polymers82,1653
Non-polymers00
Water79344
1
A: Glutathione S-transferase
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)54,7762
Polymers54,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-22 kcal/mol
Surface area17910 Å2
MethodPISA
2
C: Glutathione S-transferase

C: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)54,7762
Polymers54,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3560 Å2
ΔGint-17 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.920, 111.245, 246.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutathione S-transferase /


Mass: 27388.230 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_L_2272, Atu3701, GST / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: A9CFJ9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.3 Å3/Da / Density % sol: 46.57 % / Description: DATA ANISOTROPIC
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS, PH 6.5, 25% PEG3350, 200MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 33875 / % possible obs: 99.3 % / Observed criterion σ(I): -5 / Redundancy: 6.3 % / Biso Wilson estimate: 51.201 Å2 / Rsym value: 0.078 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.952 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28815 1056 3.2 %RANDOM
Rwork0.24304 ---
obs0.24453 32296 98.66 %-
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: 71.205 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2--2.94 Å20 Å2
3----5.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 0 44 4945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9526808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9645605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98522.183252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83215851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2481560
X-RAY DIFFRACTIONr_chiral_restr0.080.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213872
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_it3.80323014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.934832
X-RAY DIFFRACTIONr_scbond_it8.11542011
X-RAY DIFFRACTIONr_scangle_it10.79961971
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 71 -
Rwork0.318 2191 -
obs--93.86 %

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