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- PDB-5dbq: Crystal structure of insect thioredoxin at 1.95 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5dbq
TitleCrystal structure of insect thioredoxin at 1.95 Angstroms
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Thioredoxin / Disulfide bridge
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnticarsia gemmatalis (velvetbean caterpillar)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKlinke, S. / Tejedor, M.D. / Cerutti, M.L. / Giacometti, R. / Otero, L.H. / Goldbaum, F.A. / Zavala, J.A. / Wolosiuk, R.A. / Pagano, E.A.
Funding support Argentina, 2items
OrganizationGrant numberCountry
ANPCyTPICT 2011-2115 Argentina
ANPCyTPPL2-03 Argentina
CitationJournal: To Be Published
Title: Crystal structure of insect thioredoxin at 1.95 Angstroms
Authors: Klinke, S. / Tejedor, M.D. / Cerutti, M.L. / Giacometti, R. / Otero, L.H. / Goldbaum, F.A. / Zavala, J.A. / Wolosiuk, R.A. / Pagano, E.A.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)24,2762
Polymers24,2762
Non-polymers00
Water3,387188
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,1381
Polymers12,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,1381
Polymers12,1381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.710, 28.980, 79.860
Angle α, β, γ (deg.)90.00, 128.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin /


Mass: 12138.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anticarsia gemmatalis (velvetbean caterpillar)
Plasmid: pET 28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: A0A0Y0BMD0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCloning artifact GSH at the N-terminus after Thrombin cleavage.

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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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: Small Prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 27% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: PIXEL / Date: Jul 2, 2015
Details: Diffractometer: Bruker D8 QUEST, Source: IMUS Copper Microfocus, Detector: PHOTON 100
RadiationMonochromator: Helios MX multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14272 / % possible obs: 98.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.01 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
PROTEUM PLUSPROTEUM2 (Bruker)data collection
XDSdata scaling
MrBUMPphasing
MOLREPphasing
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1XWB

1xwb


Resolution: 1.95→31.33 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.9094 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.233 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 714 5 %RANDOM
Rwork0.2098 ---
obs0.2119 14272 98.37 %-
Displacement parametersBiso mean: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1-4.5697 Å20 Å2-2.0724 Å2
2---1.9105 Å20 Å2
3----2.6592 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: 1 / Resolution: 1.95→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 188 1836
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011670HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122246HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d618SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes228HARMONIC5
X-RAY DIFFRACTIONt_it1670HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion17.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2046SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.11 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2679 142 5.01 %
Rwork0.2557 2692 -
all0.2563 2834 -
obs--98.37 %

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