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- PDB-5hr2: Crystal structure of thioredoxin L94A mutant -

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Basic information

Entry
Database: PDB / ID: 5hr2
TitleCrystal structure of thioredoxin L94A mutant
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / E. coli thioredoxin / thiol-redox reaction
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Thioredoxin / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsNoguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants.
Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...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_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9043
Polymers11,7771
Non-polymers1272
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.012, 47.917, 28.878
Angle α, β, γ (deg.)90.000, 101.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

21A-685-

HOH

31A-712-

HOH

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Components

#1: Protein Thioredoxin


Mass: 11776.502 Da / Num. of mol.: 1 / Mutation: L94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, BN17_37301, ECs4714 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SKR2, UniProt: P0AA25*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The drop was a 1:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.2→28.252 Å / Num. obs: 34197 / % possible obs: 94.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.9
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 6.3 / % possible all: 81.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_2247refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEB

1keb


Resolution: 1.2→28.252 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 12.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1515 1725 5.05 %random
Rwork0.1318 63937 --
obs0.1329 34197 94.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.51 Å2 / Biso mean: 14.5451 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 1.2→28.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 2 125 940
Biso mean--15 23.33 -
Num. residues----107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011838
X-RAY DIFFRACTIONf_angle_d1.1221138
X-RAY DIFFRACTIONf_chiral_restr0.088131
X-RAY DIFFRACTIONf_plane_restr0.008146
X-RAY DIFFRACTIONf_dihedral_angle_d15.819311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21720.14791190.11321935205470
1.2172-1.23530.1251360.1072317245383
1.2353-1.25460.15581560.10762493264987
1.2546-1.27520.16591100.1052602271291
1.2752-1.29720.15581250.10652552267792
1.2972-1.32080.12991150.10792639275493
1.3208-1.34620.14771360.1122662279894
1.3462-1.37370.1351460.11242694284094
1.3737-1.40350.13791300.10712739286998
1.4035-1.43620.14121390.11042700283995
1.4362-1.47210.14571380.10762762290098
1.4721-1.51190.11881250.11312732285796
1.5119-1.55640.14891380.10992742288098
1.5564-1.60660.11591550.10752708286395
1.6066-1.6640.12351800.11342703288399
1.664-1.73060.16461550.12012747290297
1.7306-1.80940.14161590.12172739289897
1.8094-1.90480.14631360.11652791292799
1.9048-2.02410.14641490.12342758290798
2.0241-2.18030.1591480.12962779292798
2.1803-2.39960.14131620.12642793295598
2.3996-2.74660.15011470.14012758290599
2.7466-3.45940.15041370.1582832296999
3.4594-28.25980.18871610.17392760292198

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