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- PDB-2fch: Crystal Structure of Thioredoxin Mutant G74S -

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Basic information

Entry
Database: PDB / ID: 2fch
TitleCrystal Structure of Thioredoxin Mutant G74S
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / Alpha Beta
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: To be Published
Title: Crystal Structure of Thioredoxin Mutant G74S
Authors: Gavira, J.A. / Perez-Jimenez, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / exptl_crystal_grow ...database_2 / exptl_crystal_grow / 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 / _exptl_crystal_grow.method / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
C: Thioredoxin 1
D: Thioredoxin 1
E: Thioredoxin 1
F: Thioredoxin 1
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,84914
Polymers82,0227
Non-polymers8277
Water2,144119
1
A: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8362
Polymers11,7171
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7171
Polymers11,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7171
Polymers11,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0724
Polymers11,7171
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9543
Polymers11,7171
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)11,7171
Polymers11,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8362
Polymers11,7171
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
B: Thioredoxin 1
C: Thioredoxin 1
D: Thioredoxin 1
F: Thioredoxin 1
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0609
Polymers58,5875
Non-polymers4734
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-59 kcal/mol
Surface area22970 Å2
MethodPISA
9
A: Thioredoxin 1
E: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7895
Polymers23,4352
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-31 kcal/mol
Surface area10120 Å2
MethodPISA
10
B: Thioredoxin 1
C: Thioredoxin 1
D: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5076
Polymers35,1523
Non-polymers3553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-45 kcal/mol
Surface area14400 Å2
MethodPISA
11
F: Thioredoxin 1
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5533
Polymers23,4352
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-18 kcal/mol
Surface area10330 Å2
MethodPISA
12
B: Thioredoxin 1
D: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7895
Polymers23,4352
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-31 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.65, 88.80, 118.08
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thioredoxin 1 / / TRX1 / TRX


Mass: 11717.413 Da / Num. of mol.: 7 / Mutation: G74S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, fipA, tsnC / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / References: UniProt: P0AA25
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 5.4
Details: 60% (v/v) MPD, Hepes 15 mM, 1 mM Ac2Cu, pH 5.4, Counter-diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 20, 2005 / Details: Montel Optics
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→29.65 Å / Num. all: 26472 / Num. obs: 26251 / % possible obs: 99.2 % / Redundancy: 4.48 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.0465 / Net I/σ(I): 21.28
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 1.96 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1351 / Rsym value: 0.3179 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.6data extraction
PROTEUM PLUS2data reduction
SAINTdata scaling
SADABSdata scaling
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2TRX_A

Resolution: 2.6→29.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.871 / SU B: 11.143 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 1.154 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Xtalview, Molprobity were also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1328 5.1 %RANDOM
Rwork0.203 ---
all0.207 ---
obs-24866 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5659 0 56 119 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225884
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9898007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15726.553235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.681151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.353158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024298
X-RAY DIFFRACTIONr_nbd_refined0.2030.22521
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.23
X-RAY DIFFRACTIONr_mcbond_it1.29623824
X-RAY DIFFRACTIONr_mcangle_it2.00135977
X-RAY DIFFRACTIONr_scbond_it1.1322336
X-RAY DIFFRACTIONr_scangle_it1.66332030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.6-2.6670.391870.28517290.29191095.079
2.667-2.740.358930.26717540.271188098.245
2.74-2.820.3991060.26116660.269180298.335
2.82-2.9060.347880.24916820.254178799.049
2.906-3.0020.306910.22716170.231171299.766
3.002-3.1070.256890.19715840.21673100
3.107-3.2240.322740.2215320.2251606100
3.224-3.3550.2771040.20314510.2091555100
3.355-3.5040.236700.20314270.2051497100
3.504-3.6750.271690.20713520.211421100
3.675-3.8730.292620.18112990.1851361100
3.873-4.1070.205640.17912300.1811294100
4.107-4.3890.244630.17211480.1751211100
4.389-4.740.199600.14810920.1511152100
4.74-5.190.226400.1610110.1631051100
5.19-5.7980.243440.1929140.194958100
5.798-6.6880.321460.2228160.227862100
6.688-8.1730.337370.216930.216730100
8.173-11.4820.211280.1495660.152594100
11.482-29.650.308130.2823030.28436087.778

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