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- PDB-4ags: Leishmania TDR1 - a unique trimeric glutathione transferase -

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Basic information

Entry
Database: PDB / ID: 4ags
TitleLeishmania TDR1 - a unique trimeric glutathione transferase
ComponentsTHIOL-DEPENDENT REDUCTASE 1
KeywordsTRANSFERASE / LEISHMANIASIS / DE-GLUATHIONYLATION
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 / Thiol-dependent reductase 1
Similarity search - Component
Biological speciesLEISHMANIA INFANTUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFyfe, P.K. / Westrop, G.D. / Silva, A.M. / Coombs, G.H. / Hunter, W.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Leishmania Tdr1 Structure, a Unique Trimeric Glutathione Transferase Capable of Deglutathionylation and Antimonial Prodrug Activation.
Authors: Fyfe, P.K. / Westrop, G.D. / Silva, A.M. / Coombs, G.H. / Hunter, W.N.
#1: Journal: Biochem.J. / Year: 2004
Title: Reduction of Anti-Leishmanial Pentavalent Antimonial Drugs by a Parasite-Specific Thiol-Dependent Reductase, Tdr1.
Authors: Denton, H. / Mcgregor, J.C. / Coombs, G.H.
History
DepositionJan 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: THIOL-DEPENDENT REDUCTASE 1
B: THIOL-DEPENDENT REDUCTASE 1
C: THIOL-DEPENDENT REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,36224
Polymers159,5883
Non-polymers2,77521
Water20,9871165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-44.3 kcal/mol
Surface area65720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.477, 58.396, 160.385
Angle α, β, γ (deg.)90.00, 111.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4918, 0.4657, 0.7357), (-0.2641, 0.7254, -0.6357), (-0.8297, -0.5069, -0.2338)-59.45, 81.35, 163.9
2given(-0.495, -0.2704, 0.8257), (0.465, 0.7204, 0.5146), (0.734, -0.6387, -0.2309)127.9, 52.72, 133.4

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Components

#1: Protein THIOL-DEPENDENT REDUCTASE 1


Mass: 53195.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA INFANTUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834 (DE3) / References: UniProt: A4I8P2
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→29.8 Å / Num. obs: 74464 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.633 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20799 3725 5 %RANDOM
Rwork0.14889 ---
obs0.15194 70625 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.404 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å2-0.61 Å2
2--5.41 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10409 0 180 1165 11754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211610
X-RAY DIFFRACTIONr_bond_other_d0.0010.028115
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.97815750
X-RAY DIFFRACTIONr_angle_other_deg0.9093.00119618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7351458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5423.207552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.044151865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7641597
X-RAY DIFFRACTIONr_chiral_restr0.080.21604
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022508
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 264 -
Rwork0.193 4994 -
obs--98.19 %
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)
13.55880.0973-0.01373.20940.99942.732-0.0155-0.5034-0.19750.36750.2421-0.59360.40080.8045-0.22660.26570.1939-0.10510.3388-0.04090.323556.2187.889124.857
21.2153-0.3517-0.78210.48860.75321.5910.06850.02380.10760.03450.0079-0.0592-0.02140.0507-0.07630.19340.0183-0.00770.01440.02910.133629.14125.863130.227
32.8116-0.4093-0.57833.45820.21411.74260.0783-0.07150.47470.09520.0511-0.0917-0.2845-0.1559-0.12940.29410.03160.04980.0365-0.05590.226413.58245.542149.875
42.0241-0.1513-0.52651.49220.62481.9601-0.0694-0.0356-0.16270.2338-0.06790.22430.148-0.48860.13730.2389-0.02760.05680.1433-0.01730.1479-0.2720.471139.328
50.68510.16690.88510.39840.91412.8318-0.0293-0.01870.0194-0.0496-0.16330.1095-0.2215-0.54670.19270.20270.0330.02650.2266-0.04260.1804-2.73517.873107.655
61.4507-1.18030.2912.9180.52053.96050.07950.19680.1417-0.5264-0.18050.0578-0.565-0.53670.1010.2750.0878-0.0760.4478-0.11420.2284-13.28413.83578.787
71.1189-0.3246-0.12940.81371.59366.00890.05090.1264-0.30.2226-0.0395-0.01490.6026-0.1262-0.01140.2714-0.0319-0.01050.0259-0.060.236711.01-7.81283.463
82.04970.19380.43020.25750.24341.197-0.0470.0821-0.0817-0.00540.0338-0.06540.14250.10180.01330.17230.02150.01350.0126-0.01660.152829.7047.23994.978
92.20430.01640.42862.5125-1.46814.0793-0.2060.22140.180.0566-0.0937-0.4184-0.20080.85730.29980.0895-0.0053-0.00620.4385-0.01390.370665.14416.91595.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 81
2X-RAY DIFFRACTION2A82 - 358
3X-RAY DIFFRACTION3A359 - 448
4X-RAY DIFFRACTION4B5 - 110
5X-RAY DIFFRACTION5B111 - 341
6X-RAY DIFFRACTION6B342 - 444
7X-RAY DIFFRACTION7C3 - 61
8X-RAY DIFFRACTION8C65 - 339
9X-RAY DIFFRACTION9C340 - 450

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