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- PDB-9nce: Oxidized Treponema pallidum thioredoxin strain Nichols -

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Basic information

Entry
Database: PDB / ID: 9nce
TitleOxidized Treponema pallidum thioredoxin strain Nichols
ComponentsThioredoxin
KeywordsSTRUCTURAL PROTEIN / Salvarsan / Mapharsen / arsenic / thioredoxin / thioredoxin reductase
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin family active site. / Thioredoxin, conserved site / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Thioredoxin
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum str. Nichols (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsCarbone, V. / Ronimus, R.S. / Sutherland-Smith, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural examination of thioredoxin and thioredoxin reductase from the syphilis organism Treponema pallidum with Mapharsen, the active ingredient of the original magic bullet (Salvarsan).
Authors: Carbone, V. / Ronimus, R.S.
History
DepositionFeb 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5483
Polymers15,4181
Non-polymers1302
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.820, 89.820, 33.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin / Trx


Mass: 15417.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum str. Nichols (bacteria)
Gene: trxA, TP_0919 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O83889
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaCl, 0.1M Na+/K+ phosphate PH 6.2, 50% v/v PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.96→89.82 Å / Num. obs: 10426 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Χ2: 0.92 / Net I/σ(I): 14.8 / Num. measured all: 97225
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 1.264 / Num. measured all: 6581 / Num. unique obs: 717 / CC1/2: 0.862 / Rpim(I) all: 0.434 / Rrim(I) all: 1.338 / Χ2: 0.69 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→63.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.522 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 488 4.7 %RANDOM
Rwork0.19997 ---
obs0.20258 9903 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.581 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å2-0 Å2-0 Å2
2---3.37 Å20 Å2
3---6.73 Å2
Refinement stepCycle: 1 / Resolution: 1.96→63.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 6 26 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012816
X-RAY DIFFRACTIONr_bond_other_d0.0010.016802
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.7861111
X-RAY DIFFRACTIONr_angle_other_deg0.6571.7581855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.40452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6310146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7534.194420
X-RAY DIFFRACTIONr_mcbond_other3.7464.195420
X-RAY DIFFRACTIONr_mcangle_it4.6777.497525
X-RAY DIFFRACTIONr_mcangle_other4.6737.495526
X-RAY DIFFRACTIONr_scbond_it5.9414.747396
X-RAY DIFFRACTIONr_scbond_other5.5134.701392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3178.434581
X-RAY DIFFRACTIONr_long_range_B_refined8.28840.62868
X-RAY DIFFRACTIONr_long_range_B_other7.92539.86867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.962→2.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 36 -
Rwork0.391 706 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -25.6586 Å / Origin y: -5.754 Å / Origin z: -1.3287 Å
111213212223313233
T0.0221 Å20.0142 Å2-0.0003 Å2-0.0227 Å20.0062 Å2--0.0623 Å2
L6.2589 °2-1.8572 °20.3278 °2-3.9603 °2-0.7604 °2--3.2367 °2
S-0.0556 Å °0.2031 Å °0.3864 Å °-0.0022 Å °-0.0082 Å °-0.4712 Å °0.1993 Å °0.2113 Å °0.0638 Å °

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