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- PDB-2vps: Structure Of The Bifunctional Leishmania Major Trypanothione Synt... -

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Basic information

Entry
Database: PDB / ID: 2vps
TitleStructure Of The Bifunctional Leishmania Major Trypanothione Synthetase-Amidase
ComponentsTRYPANOTHIONE SYNTHETASE
KeywordsLIGASE
Function / homology
Function and homology information


trypanothione synthase / trypanothione synthase activity / ligase activity / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #330 / : / Glutathionylspermidine synthase, pre-ATP-grasp-like domain / Glutathionylspermidine synthase preATP-grasp / CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Pre-ATP-grasp domain superfamily ...Dna Ligase; domain 1 - #330 / : / Glutathionylspermidine synthase, pre-ATP-grasp-like domain / Glutathionylspermidine synthase preATP-grasp / CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Pre-ATP-grasp domain superfamily / Dna Ligase; domain 1 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Trypanothione synthetase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsFyfe, P.K. / Oza, S.L. / Fairlamb, A.H. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Leishmania Trypanothione Synthetase-Amidase Structure Reveals a Basis for Regulation of Conflicting Synthetic and Hydrolytic Activities.
Authors: Fyfe, P.K. / Oza, S.L. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionMar 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPANOTHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8678
Polymers74,5301
Non-polymers3377
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.050, 85.600, 168.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPANOTHIONE SYNTHETASE


Mass: 74530.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PET15B-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q711P7, trypanothione synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.4 Å3/Da / Density % sol: 64 %
Description: SEARCH MODEL WAS MONOMER A SELECTED FROM PDB ENTRY 2VOB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97897
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 96640 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.5 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VOB

2vob


Resolution: 2.75→28.33 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.973 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1363 5 %RANDOM
Rwork0.204 ---
obs0.207 25883 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20 Å2
2---2.51 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.75→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 7 45 4939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225024
X-RAY DIFFRACTIONr_bond_other_d0.0010.023431
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9356816
X-RAY DIFFRACTIONr_angle_other_deg0.90238295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1945599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60323.923260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03315817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7421532
X-RAY DIFFRACTIONr_chiral_restr0.170.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
X-RAY DIFFRACTIONr_nbd_refined0.2170.21023
X-RAY DIFFRACTIONr_nbd_other0.1930.23510
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22411
X-RAY DIFFRACTIONr_nbtor_other0.0880.22622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7191.53875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84724834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16132434
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.744.51982
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: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.414 95
Rwork0.325 1793
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)
10.98990.22720.47291.2474-0.65681.9053-0.05320.22920.30250.0895-0.0086-0.029-0.11220.01270.0618-0.21750.06160.0428-0.10110.1341-0.061-4.63223.5717.771
21.1610.75170.62234.2020.91611.69720.0460.0557-0.18390.04750.1126-0.58490.12290.2941-0.1586-0.06910.07-0.0552-0.16250.0096-0.13614.8223.87136.363
32.6233-0.1416-0.78847.85850.28331.38190.04070.0780.0101-0.72460.006-0.64310.25760.2736-0.04660.11020.03810.0013-0.0974-0.0194-0.21352.432-6.4723.514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 214
2X-RAY DIFFRACTION2A215 - 586
3X-RAY DIFFRACTION3A587 - 652

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