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

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Basic information

Entry
Database: PDB / ID: 2eiq
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
COPPER (II) ION / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7426
Polymers23,3792
Non-polymers3634
Water2,198122
1
A: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8713
Polymers11,6891
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8713
Polymers11,6891
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Thioredoxin 1
hetero molecules

A: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7426
Polymers23,3792
Non-polymers3634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2420 Å2
ΔGint-52 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.209, 49.557, 59.427
Angle α, β, γ (deg.)90.00, 113.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin 1 / TRX1 / TRX / THIOREDOXIN 6P


Mass: 11689.427 Da / Num. of mol.: 2 / Mutation: T89C
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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 40% MPD, 1MM CUPRIC ACETATE, 10MM SODIUM ACETATE, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: May 16, 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: 1.9→54.55 Å / Num. all: 18923 / Num. obs: 18812 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.304 / Rsym value: 0.304 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 1.9→41.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.996 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21845 1930 10.3 %RANDOM
Rwork0.18374 ---
obs0.18731 16882 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.29 Å2
2--1.05 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 18 122 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221677
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9942274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9515212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.95126.66766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.566152
X-RAY DIFFRACTIONr_chiral_restr0.1110.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021230
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21134
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3940.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.51094
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88421701
X-RAY DIFFRACTIONr_scbond_it2.983665
X-RAY DIFFRACTIONr_scangle_it4.594.5573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 161 -
Rwork0.208 1181 -
obs--97.18 %

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