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- PDB-3dyr: Crystal structure of E. coli thioredoxin mutant I76T in its oxidi... -

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Basic information

Entry
Database: PDB / ID: 3dyr
TitleCrystal structure of E. coli thioredoxin mutant I76T in its oxidized form
ComponentsThioredoxin-1
KeywordsELECTRON TRANSPORT / mutant protein / Host-virus interaction / Redox-active center / Transport
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsRen, G. / Bardwell, J.C.A. / Xu, Z.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Properties of the thioredoxin fold superfamily are modulated by a single amino acid residue.
Authors: Ren, G. / Stephan, D. / Xu, Z. / Zheng, Y. / Tang, D. / Harrison, R.S. / Kurz, M. / Jarrott, R. / Shouldice, S.R. / Hiniker, A. / Martin, J.L. / Heras, B. / Bardwell, J.C.
History
DepositionJul 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-1
B: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)23,7492
Polymers23,7492
Non-polymers00
Water2,432135
1
A: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,8751
Polymers11,8751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,8751
Polymers11,8751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.790, 39.390, 90.550
Angle α, β, γ (deg.)90.000, 96.630, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin-1 / Trx-1


Mass: 11874.540 Da / Num. of mol.: 2 / Mutation: I76T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.19 Å3/Da / Density % sol: 43.9 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 2, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13739 / % possible obs: 97 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.059
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.073.10.24994.7
2.07-2.153.20.19695.7
2.15-2.253.20.14896.5
2.25-2.373.20.11696.6
2.37-2.523.20.09497.3
2.52-2.713.30.07597.2
2.71-2.993.30.06497.4
2.99-3.423.30.05198.2
3.42-4.313.20.04698.1
4.31-503.20.04898.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.649 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.41 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 1071 8.03 %
Rwork0.2512 --
obs0.2544 13345 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.456 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 26.229 Å2
Baniso -1Baniso -2Baniso -3
1--3.378 Å2-0 Å22.172 Å2
2---1.491 Å2-0 Å2
3---4.869 Å2
Refinement stepCycle: LAST / Resolution: 2→25.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 135 1733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071632
X-RAY DIFFRACTIONf_angle_d1.0382222
X-RAY DIFFRACTIONf_dihedral_angle_d17.898564
X-RAY DIFFRACTIONf_chiral_restr0.064265
X-RAY DIFFRACTIONf_plane_restr0.005286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0890.3481290.2591429155888
2.089-2.20.3461250.2411470159591
2.2-2.3370.3271280.2391498162693
2.337-2.5180.3311380.2421528166694
2.518-2.7710.3281360.2621502163894
2.771-3.1710.2911410.2621568170997
3.171-3.9930.2411220.2291626174898
3.993-25.6510.2431520.2491653180598

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