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- PDB-3lg6: Crystal structure of putative glutathione transferase from Coccid... -

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Basic information

Entry
Database: PDB / ID: 3lg6
TitleCrystal structure of putative glutathione transferase from Coccidioides immitis
Componentsputative glutathione transferase
KeywordsTRANSFERASE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ALS Collaborative Crystallography / pathogenic fungus / coccidioidomycosis / Valley Fever / meningitis
Function / homology
Function and homology information


aromatic amino acid metabolic process / glutathione transferase / glutathione transferase activity / cytoplasm
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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...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 / 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
Probable glutathione S-transferase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
DepositionJan 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: putative glutathione transferase
B: putative glutathione transferase
C: putative glutathione transferase
D: putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0398
Polymers103,6554
Non-polymers3844
Water10,629590
1
A: putative glutathione transferase
B: putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0194
Polymers51,8272
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-60 kcal/mol
Surface area18900 Å2
MethodPISA
2
C: putative glutathione transferase
D: putative glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0194
Polymers51,8272
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-60 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.740, 99.640, 184.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 4 - 231 / Label seq-ID: 8 - 235

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
putative glutathione transferase


Mass: 25913.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: D2YW48*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: CSHT screen condition B5, 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30% PEG 4000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 206458b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 49300 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.23
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3520 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å29.64 Å
Translation3 Å29.64 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CZ2

2cz2


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 10.947 / SU ML: 0.127 / SU R Cruickshank DPI: 0.254 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2492 5.1 %RANDOM
Rwork0.171 ---
obs0.173 49231 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.8 Å2 / Biso mean: 23.357 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--1.34 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6834 0 20 590 7444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227010
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9749572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59623.737281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.615151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4081548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215264
X-RAY DIFFRACTIONr_mcbond_it0.7671.54493
X-RAY DIFFRACTIONr_mcangle_it1.44227274
X-RAY DIFFRACTIONr_scbond_it2.47732517
X-RAY DIFFRACTIONr_scangle_it3.9694.52295
Refine LS restraints NCS

Ens-ID: 1 / Number: 1601 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.445
2BLOOSE POSITIONAL0.445
3CLOOSE POSITIONAL0.415
4DLOOSE POSITIONAL0.455
1ALOOSE THERMAL3.4210
2BLOOSE THERMAL2.1310
3CLOOSE THERMAL2.4410
4DLOOSE THERMAL3.2610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 194 -
Rwork0.252 3323 -
all-3517 -
obs--97.94 %
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)
10.8045-0.0676-0.05740.4966-0.14491.24880.00120.0389-0.11630.0224-0.0102-0.0320.0606-0.02440.00910.0051-0.0035-0.00480.0303-0.00740.0555-4.9054-15.094311.9082
21.20140.02150.46230.69950.02391.3565-0.076-0.02060.21860.03220.01360.0145-0.2169-0.03160.06240.04150.0032-0.02180.01490.00950.0722-16.01325.298711.3271
30.80060.0445-0.08050.68480.01112.88850.0639-0.0119-0.07960.0131-0.02930.01680.2298-0.1634-0.03460.0303-0.0129-0.01780.01660.00110.0211-16.9039-19.393153.417
40.77240.0246-0.14950.81520.30392.40620.1052-0.0340.14-0.0877-0.0099-0.0046-0.5040.1336-0.09520.1223-0.0210.02520.0284-0.02270.0368-10.0982.494357.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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