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- PDB-3lsz: Crystal structure of glutathione s-transferase from Rhodobacter s... -

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Basic information

Entry
Database: PDB / ID: 3lsz
TitleCrystal structure of glutathione s-transferase from Rhodobacter sphaeroides
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / xenobiotic / biodegradative metabolism / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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 / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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 speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of glutathione s-transferase from Rhodobacter sphaeroides
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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)101,54514
Polymers99,6434
Non-polymers1,90210
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-34 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.920, 50.398, 133.228
Angle α, β, γ (deg.)90.00, 125.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-294-

HOH

21D-391-

HOH

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Components

#1: Protein
Glutathione S-transferase


Mass: 24910.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023, 2.4.1 / Gene: RHOS4_23800, RSP_0769 / Plasmid: Codon+RIL - Stratagene / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IZT6
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 46.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350; 0.2M Ammonium Acetate; 0.1M Bis-Tris pH 6.5 and glutathione, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 95616 / Num. obs: 95616 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.364 / Num. unique all: 4572 / % possible all: 67.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3747 -RANDOM
Rwork0.2061 ---
all-93502 --
obs-93502 93.2 %-
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å22.2 Å2
2---3.42 Å20 Å2
3---2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6732 0 124 414 7270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.261 474 -
Rwork0.247 --
obs-11204 70.3 %

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