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- PDB-2vob: TRYPANOTHIONE SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 2vob
TitleTRYPANOTHIONE SYNTHETASE
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
Trypanothione synthetase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionFeb 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
B: TRYPANOTHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1314
Polymers149,0602
Non-polymers712
Water10,863603
1
A: TRYPANOTHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5652
Polymers74,5301
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRYPANOTHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5652
Polymers74,5301
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.120, 127.710, 88.790
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRYPANOTHIONE SYNTHETASE


Mass: 74530.016 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.6 Å3/Da / Density % sol: 50 %
Description: FOR DETAILS OF THE MOLECULAR REPLACEMENT MODEL SEE MANUSCRIPT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97548
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97548 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 65387 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.5 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0027refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.327 / SU ML: 0.159 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3304 5 %RANDOM
Rwork0.19 ---
obs0.193 62766 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20.71 Å2
2---0.38 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9669 0 2 603 10274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210158
X-RAY DIFFRACTIONr_bond_other_d0.0010.026957
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.93413805
X-RAY DIFFRACTIONr_angle_other_deg0.901316819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.42151220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47123.816532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.348151652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4381568
X-RAY DIFFRACTIONr_chiral_restr0.0840.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022217
X-RAY DIFFRACTIONr_nbd_refined0.1990.21894
X-RAY DIFFRACTIONr_nbd_other0.1930.27238
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24779
X-RAY DIFFRACTIONr_nbtor_other0.0850.25254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2622
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.57862
X-RAY DIFFRACTIONr_mcbond_other0.141.52433
X-RAY DIFFRACTIONr_mcangle_it1.08929766
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54834943
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2184.54039
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→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 242 -
Rwork0.207 4599 -
obs--100 %
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)
13.2195-1.9666-0.65691.28460.80022.04230.05680.12770.1515-0.0467-0.1013-0.0471-0.15190.00470.0445-0.2787-0.0329-0.0158-0.19290.0055-0.19798.771-43.29-21.68
20.5050.2983-0.32512.5731-0.36671.84460.0297-0.05470.08290.191-0.08630.0339-0.2854-0.07520.0566-0.14930.0449-0.0372-0.1807-0.0459-0.1905-11.731-17.697-5.46
35.7698-2.19791.83732.6745-0.73383.634-0.1553-0.442-0.26860.4130.1666-0.04850.27680.4292-0.0113-0.0389-0.0237-0.0621-0.0913-0.0279-0.08361.837-29.982.37
42.8789-1.51050.46622.1654-0.62621.75190.0050.0306-0.1727-0.18530.03380.250.2336-0.1683-0.0388-0.2425-0.055-0.0052-0.15180.0191-0.1592-40.9777.90116.012
50.38960.26460.12592.08921.15263.1467-0.0667-0.1434-0.19410.41520.02150.15860.6681-0.13210.04510.10650.04030.0808-0.07330.0644-0.1187-28.615-18.30337.287
63.51710.15060.59841.30490.63172.419-0.1571-0.31890.07710.35840.08630.5081-0.0089-1.00840.07070.10990.05720.16080.18390.01370.0796-41.397-6.47343.337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 214
2X-RAY DIFFRACTION2A215 - 586
3X-RAY DIFFRACTION3A587 - 652
4X-RAY DIFFRACTION4B5 - 214
5X-RAY DIFFRACTION5B215 - 586
6X-RAY DIFFRACTION6B587 - 652

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