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- PDB-2eio: Design of Disulfide-linked Thioredoxin Dimers and Multimers Throu... -

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Basic information

Entry
Database: PDB / ID: 2eio
TitleDesign of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / THIOREDOXIN / MUTANT / DI-SULFIDE BOND
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKobayashi, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Authors: Das, M. / Kobayashi, M. / Yamada, Y. / Sreeramulu, S. / Ramakrishnan, C. / Wakatsuki, S. / Kato, R. / Varadarajan, R.
History
DepositionMar 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
C: Thioredoxin 1
D: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)46,6464
Polymers46,6464
Non-polymers00
Water1,02757
1
A: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.731, 59.209, 75.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Thioredoxin 1 / TRX1 / TRX / THIOREDOXIN 11P


Mass: 11661.417 Da / Num. of mol.: 4 / Mutation: E101C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.1M TRIS, 0.2M MAGNESIUM CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14472 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 24.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.258 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 2.6→38.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 148038.94 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1405 9.9 %RANDOM
Rwork0.231 ---
obs0.231 14183 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.8641 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å20 Å2
2--9.32 Å20 Å2
3----5.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 57 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 196 8.9 %
Rwork0.248 2013 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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