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- PDB-2i4a: Crystal structure of thioredoxin from the acidophile Acetobacter aceti -

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Basic information

Entry
Database: PDB / ID: 2i4a
TitleCrystal structure of thioredoxin from the acidophile Acetobacter aceti
Componentsthioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / acidophile / disulfide exchange
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / BETA-MERCAPTOETHANOL
Function and homology information
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsStarks, C.M. / Kappock, T.J.
CitationJournal: Protein Sci. / Year: 2007
Title: Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti.
Authors: Starks, C.M. / Francois, J.A. / Macarthur, K.M. / Heard, B.Z. / Kappock, T.J.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6472
Polymers11,5691
Non-polymers781
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.940, 42.240, 63.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There is one monomer in the asymmetric unit.

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Components

#1: Protein thioredoxin


Mass: 11569.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Plasmid: pET-23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: microseeding in 100 mM sodium acetate (pH 4.6), 100 mM ammonium acetate, 24% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 15, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1→42.24 Å / Num. obs: 48392 / % possible obs: 96.2 % / Redundancy: 6.13 % / Biso Wilson estimate: 7.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 23.9
Reflection shellResolution: 1→1.04 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3351 / Rsym value: 0.479 / % possible all: 67.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
JBluIce-EPICSdata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2trx

2trx


Resolution: 1→35.2 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.588 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS USING MOLPROBITY
RfactorNum. reflection% reflectionSelection details
Rfree0.1582 2428 5 %RANDOM
Rwork0.13346 ---
all0.13465 ---
obs0.13465 45895 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 4 175 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022845
X-RAY DIFFRACTIONr_bond_other_d0.0010.02859
X-RAY DIFFRACTIONr_angle_refined_deg2.1921.9761144
X-RAY DIFFRACTIONr_angle_other_deg1.00731970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08126.12931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3815155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.105152
X-RAY DIFFRACTIONr_chiral_restr0.1460.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
X-RAY DIFFRACTIONr_nbd_refined0.2230.2159
X-RAY DIFFRACTIONr_nbd_other0.1950.2902
X-RAY DIFFRACTIONr_nbtor_refined0.180.2430
X-RAY DIFFRACTIONr_nbtor_other0.0980.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7111.5561
X-RAY DIFFRACTIONr_mcbond_other0.9651.5218
X-RAY DIFFRACTIONr_mcangle_it3.3742866
X-RAY DIFFRACTIONr_scbond_it4.9733344
X-RAY DIFFRACTIONr_scangle_it6.8044.5278
X-RAY DIFFRACTIONr_rigid_bond_restr2.30731881
X-RAY DIFFRACTIONr_sphericity_free15.3633175
X-RAY DIFFRACTIONr_sphericity_bonded5.44331688
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 135 -
Rwork0.38 2219 -
obs-2354 64.25 %

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