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- PDB-3h79: Crystal structure of Trypanosoma cruzi thioredoxin-like hypotheti... -

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Basic information

Entry
Database: PDB / ID: 3h79
TitleCrystal structure of Trypanosoma cruzi thioredoxin-like hypothetical protein Q4DV70
ComponentsThioredoxin-like protein
KeywordsUNKNOWN FUNCTION / thioredoxin fold / catalytic cysteines missing
Function / homologyThioredoxin / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / THIOCYANATE ION / Thioredoxin domain-containing protein
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSantos, C.R. / Fessel, M.R. / Vieira, L.C. / Krieger, M.A. / Goldenberg, S. / Guimaraes, B.G. / Zanchin, N.I.T. / Barbosa, J.A.R.G.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Trypanosoma cruzi thioredoxin-like hypothetical protein Q4DV70
Authors: Santos, C.R. / Fessel, M.R. / Vieira, L.C. / Krieger, M.A. / Goldenberg, S. / Guimaraes, B.G. / Zanchin, N.I.T. / Barbosa, J.A.R.G.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999author states that the sequence conflict at residue 94 is likely due to the strain variation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9442
Polymers14,8861
Non-polymers581
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.042, 50.321, 61.179
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 Thioredoxin-like protein


Mass: 14885.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Dm28c
Gene: Tc00.1047053508173.160, Trypanosoma cruzi strain CL Brener hypothetical protein partial mRNA
Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)slyD- / References: UniProt: Q4DV70
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.81 Å3/Da / Density % sol: 32.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 25% PEG 1500, 0.2M sodium thiocyanate, 0.01M phenol, 10% ethyleneglycol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 17813 / Num. obs: 17813 / % possible obs: 99.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1619 / % possible all: 95.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B5E

2b5e


Resolution: 1.5→19.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.875 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22361 880 5 %RANDOM
Rwork0.18 ---
obs0.18209 16892 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.63 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 3 116 1084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9491375
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87722.41458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2221513
X-RAY DIFFRACTIONr_chiral_restr0.1680.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021794
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4241.5580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2132954
X-RAY DIFFRACTIONr_scbond_it3.3013440
X-RAY DIFFRACTIONr_scangle_it5.0254.5421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 65 -
Rwork0.316 1159 -
obs--94.74 %
Refinement TLS params.Method: refined / Origin x: 9.9112 Å / Origin y: 0.8025 Å / Origin z: -9.6849 Å
111213212223313233
T0.0195 Å2-0.0019 Å20.0065 Å2-0.0197 Å2-0.0017 Å2--0.004 Å2
L1.742 °2-0.4256 °2-0.0698 °2-1.2164 °20.1979 °2--0.6072 °2
S-0.0095 Å °-0.0199 Å °-0.0009 Å °0.0366 Å °-0.0174 Å °-0.0044 Å °0.0114 Å °0.031 Å °0.0269 Å °

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