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- PDB-9ncg: Marpharsen treated Treponema pallidum thioredoxin strain Nichols -

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Basic information

Entry
Database: PDB / ID: 9ncg
TitleMarpharsen treated 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
3-HYDROXY-PROPANOIC ACID / Thioredoxin
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum str. Nichols (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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. / Sutherland-Smith, A.J.
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)15,5082
Polymers15,4181
Non-polymers901
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.050, 89.050, 35.176
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-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Nacl, 0.1M Na+/K+ phosphate 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: 2.64→44.53 Å / Num. obs: 4498 / % possible obs: 99.4 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Χ2: 1.07 / Net I/σ(I): 33.6 / Num. measured all: 38682
Reflection shellResolution: 2.64→2.76 Å / % possible obs: 99.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.543 / Num. measured all: 5021 / Num. unique obs: 586 / CC1/2: 0.954 / Rpim(I) all: 0.203 / Rrim(I) all: 0.582 / Χ2: 1.36 / Net I/σ(I) obs: 6.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→39.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 27.259 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25464 220 4.9 %RANDOM
Rwork0.20892 ---
obs0.21116 4240 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.951 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å2-0 Å2-0 Å2
2---4.03 Å20 Å2
3---8.05 Å2
Refinement stepCycle: 1 / Resolution: 2.64→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 6 3 800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.012807
X-RAY DIFFRACTIONr_bond_other_d0.0010.016801
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.7891094
X-RAY DIFFRACTIONr_angle_other_deg0.5671.7541853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8955103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.52552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53110145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02155
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_it3.0414.272415
X-RAY DIFFRACTIONr_mcbond_other3.0414.271415
X-RAY DIFFRACTIONr_mcangle_it4.5437.667517
X-RAY DIFFRACTIONr_mcangle_other4.5397.665518
X-RAY DIFFRACTIONr_scbond_it3.8734.624392
X-RAY DIFFRACTIONr_scbond_other3.8684.625393
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0658.42578
X-RAY DIFFRACTIONr_long_range_B_refined7.23340.48864
X-RAY DIFFRACTIONr_long_range_B_other7.22940.48865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.704 Å
RfactorNum. reflection% reflection
Rfree0.459 12 -
Rwork0.447 316 -
obs--98.8 %
Refinement TLS params.Method: refined / Origin x: 5.2979 Å / Origin y: -25.3288 Å / Origin z: 7.4854 Å
111213212223313233
T0.0394 Å2-0.0237 Å20.0065 Å2-0.0621 Å2-0.0041 Å2--0.05 Å2
L3.6095 °21.1888 °21.0461 °2-5.7505 °20.9698 °2--3.5191 °2
S0.0068 Å °-0.0268 Å °0.4063 Å °-0.0834 Å °-0.0869 Å °0.2405 Å °-0.2429 Å °0.0728 Å °0.0801 Å °

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