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- PDB-4fyu: Crystal structure of Thioredoxin from Wuchereria bancrofti at 2.0... -

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Basic information

Entry
Database: PDB / ID: 4fyu
TitleCrystal structure of Thioredoxin from Wuchereria bancrofti at 2.0 Angstrom
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / five parallel and anti parallel beta sheet
Function / homology
Function and homology information


sensory perception / photoreceptor cell maintenance
Similarity search - Function
Nucleoredoxin-like protein 2 / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thioredoxin
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYousef, N. / Prabhu, P. / Ahmed, A. / Iqbal, S. / Betzel, C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Thioredoxin from Wuchereria bancrofti at 2.0 Angstrom
Authors: Nasser, Y. / Prabhu, P. / Ahmed, A. / Iqbal, S. / Betzel, C.
History
DepositionJul 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Thioredoxin
B: Thioredoxin
C: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8617
Polymers48,4513
Non-polymers4104
Water6,287349
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3483
Polymers16,1501
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3633
Polymers16,1501
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,1501
Polymers16,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Thioredoxin
hetero molecules

B: Thioredoxin
hetero molecules

C: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)48,8617
Polymers48,4513
Non-polymers4104
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.610, 112.610, 162.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Thioredoxin


Mass: 16150.265 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuchereria bancrofti (agent of lymphatic filariasis)
Gene: TRX, trx-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8ISA0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM Tris HCL pH 5.6, 200mM NaCl, 24% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 35142 / % possible obs: 97 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1 / Redundancy: 4.3 %

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.474 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1771 5 %RANDOM
Rwork0.17 ---
obs0.173 33371 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å20 Å2
2--0.58 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 27 349 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193475
X-RAY DIFFRACTIONr_bond_other_d0.0010.023274
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.9584705
X-RAY DIFFRACTIONr_angle_other_deg0.9863.0027567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48425.742155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.876156
X-RAY DIFFRACTIONr_chiral_restr0.1580.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
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_it1.1111.52155
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90623470
X-RAY DIFFRACTIONr_scbond_it3.38731320
X-RAY DIFFRACTIONr_scangle_it4.8624.51235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 127 -
Rwork0.216 2196 -
obs--90.6 %

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