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- PDB-2i1u: Mycobacterium tuberculosis thioredoxin C -

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Basic information

Entry
Database: PDB / ID: 2i1u
TitleMycobacterium tuberculosis thioredoxin C
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / Thioredoxin / Redox Protein
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / peptidoglycan-based cell wall / electron transfer activity / extracellular region ...Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / peptidoglycan-based cell wall / electron transfer activity / extracellular region / plasma membrane / 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
Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHall, G. / McEwan, P.A. / Emsley, J.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structure of Mycobacterium tuberculosisthioredoxin C.
Authors: Hall, G. / Shah, M. / McEwan, P.A. / Laughton, C. / Stevens, M. / Westwell, A. / Emsley, J.
History
DepositionAug 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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


Theoretical massNumber of molelcules
Total (without water)13,1601
Polymers13,1601
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.478, 29.225, 30.954
Angle α, β, γ (deg.)88.37, 88.15, 66.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thioredoxin / TRX / MPT46


Mass: 13160.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trxA, trx, trxC / Plasmid: pTrcHisA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A616, UniProt: P9WG67*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% iso-propanol, 0.1M Na HEPES, 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21731
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONESRF ID2920.968
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATESep 4, 2004
ADSC QUANTUM 42CCDOct 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9681
ReflectionResolution: 1.3→30 Å / Num. all: 19858 / Num. obs: 19858 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.37 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2trx

2trx


Resolution: 1.3→18.9 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.45 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24032 1371 6.9 %RANDOM
Rwork0.21174 ---
obs0.21391 18487 94.73 %-
all-19858 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20.01 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 0 157 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9751237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82425.48431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27415150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.64154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02672
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.2483
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2652
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3021.5606
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1152977
X-RAY DIFFRACTIONr_scbond_it1.9743325
X-RAY DIFFRACTIONr_scangle_it3.0224.5260
X-RAY DIFFRACTIONr_rigid_bond_restr1.2873931
X-RAY DIFFRACTIONr_sphericity_free3.0923160
X-RAY DIFFRACTIONr_sphericity_bonded2.7243874
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 71 -
Rwork0.283 1379 -
obs--91.14 %

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