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- PDB-3n5o: Crystal structure of putative glutathione transferase from Coccid... -

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Basic information

Entry
Database: PDB / ID: 3n5o
TitleCrystal structure of putative glutathione transferase from Coccidioides immitis bound to glutathione
Componentsglutathione transferase
KeywordsTRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / GST / glutathione / pathogenic fungus / coccidioidomycosis / Valley Fever / meningitis
Function / homology
Function and homology information


maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrion
Similarity search - Function
Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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 / Probable glutathione S-transferase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / M.R. / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of a putative zeta-class glutathione S-transferase from the pathogenic fungus Coccidioides immitis.
Authors: Edwards, T.E. / Bryan, C.M. / Leibly, D.J. / Dieterich, S.H. / Abendroth, J. / Sankaran, B. / Sivam, D. / Staker, B.L. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4236
Polymers51,8272
Non-polymers5964
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-89 kcal/mol
Surface area17830 Å2
MethodPISA
2
A: glutathione transferase
B: glutathione transferase
hetero molecules

A: glutathione transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,84612
Polymers103,6554
Non-polymers1,1918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area12710 Å2
ΔGint-208 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.610, 110.930, 168.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-528-

HOH

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Components

#1: Protein glutathione transferase


Mass: 25913.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Gene: COI / Production host: Escherichia coli (E. coli) / References: UniProt: D2YW48
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 23.9 mg/mL protein, 0.2 M ammonium sulfate, 30% PEG 8000, 25% ethylene glycol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 40173 / Num. obs: 39710 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.509 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.78
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 5031 / Num. unique all: 2926 / Num. unique obs: 2590 / % possible all: 88.5

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Phasing

PhasingMethod: M.R.
Phasing MRRfactor: 36.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å30.84 Å
Translation3.2 Å30.84 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LG6

3lg6


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.14 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.89 / SU B: 5.782 / SU ML: 0.079 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1985 5 %RANDOM
Rwork0.158 ---
obs0.16 39566 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.75 Å2 / Biso mean: 15.886 Å2 / Biso min: 3.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 35 460 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223544
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9824838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52523.63146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4241527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212667
X-RAY DIFFRACTIONr_mcbond_it0.7491.52235
X-RAY DIFFRACTIONr_mcangle_it1.29823630
X-RAY DIFFRACTIONr_scbond_it2.24531309
X-RAY DIFFRACTIONr_scangle_it3.6434.51203
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 136 -
Rwork0.247 2447 -
all-2583 -
obs--88.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2631-0.0279-0.05590.34670.00120.29120.0324-0.01060.039-0.02740.004-0.0154-0.0597-0.0369-0.03640.02510.00750.01220.00630.00190.0150.789625.239817.4611
20.0946-0.0272-0.0330.2041-0.00660.46750.0066-0.0134-0.0138-0.00010.0116-0.04620.04010.0037-0.01810.00570.0023-0.00410.0205-0.00620.01969.11074.457722.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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