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- PDB-3ul3: Structural insights into thioredoxin-2: a component of malaria pa... -

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Basic information

Entry
Database: PDB / ID: 3ul3
TitleStructural insights into thioredoxin-2: a component of malaria parasite protein secretion machinery
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / PTEX
Function / homology
Function and homology information


PTEX complex / symbiont-containing vacuole / symbiont-containing vacuole membrane / protein-disulfide reductase activity / mitochondrion / membrane / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.905 Å
AuthorsSharma, A. / Sharma, A. / Dixit, S. / Sharma, A.
CitationJournal: Sci Rep / Year: 2011
Title: Structural insights into thioredoxin-2: a component of malaria parasite protein secretion machinery.
Authors: Sharma, A. / Sharma, A. / Dixit, S. / Sharma, A.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Thioredoxin
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)30,0682
Polymers30,0682
Non-polymers00
Water54030
1
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)15,0341
Polymers15,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)15,0341
Polymers15,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.046, 87.046, 90.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thioredoxin / / Thioredoxin-2


Mass: 15033.751 Da / Num. of mol.: 2 / Fragment: UNP residues 29-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: MAL13P1.225, trx2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 DE3 / References: UniProt: Q8IDP4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.8 % / Mosaicity: 0.364 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.125M Bis-tris pH 5.5, 2.2M ammonium sulfate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.07 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 29.23 / Number: 32987 / Rmerge(I) obs: 0.04 / Χ2: 0.93 / D res high: 2.9 Å / D res low: 100 Å / Num. obs: 8947 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.2510094.310.0180.6883.5
4.966.2597.410.0270.8913.6
4.334.9698.710.0371.3983.7
3.944.3398.310.0451.3123.7
3.653.949910.04813.7
3.443.6598.710.0620.8373.7
3.273.4499.210.1040.8493.7
3.123.2798.310.1640.7953.7
33.1299.210.2450.8163.7
2.9399.110.3660.7453.7
ReflectionResolution: 2.9→100 Å / Num. obs: 8947 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Χ2: 0.933 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.70.3668770.745199.1
3-3.123.70.2459000.816199.2
3.12-3.273.70.1648670.795198.3
3.27-3.443.70.1048860.849199.2
3.44-3.653.70.0628880.837198.7
3.65-3.943.70.0489091199
3.94-4.333.70.0458831.312198.3
4.33-4.963.70.0378941.398198.7
4.96-6.253.60.0279110.891197.4
6.25-1003.50.0189320.688194.3

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2.905→39.256 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.8 / σ(F): 0.14 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2976 871 10.09 %
Rwork0.2571 --
obs0.2612 8635 94.67 %
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 110.73 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 173.45 Å2 / Biso mean: 90.2451 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.3982 Å2-0 Å20 Å2
2--0.3982 Å2-0 Å2
3----0.7964 Å2
Refinement stepCycle: LAST / Resolution: 2.905→39.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 0 30 1621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0251624
X-RAY DIFFRACTIONf_angle_d1.6882173
X-RAY DIFFRACTIONf_chiral_restr0.121246
X-RAY DIFFRACTIONf_plane_restr0.007266
X-RAY DIFFRACTIONf_dihedral_angle_d23.275609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9051-3.08710.3641310.36751175130688
3.0871-3.32530.37641430.3391243138693
3.3253-3.65970.35851410.30781292143396
3.6597-4.18880.2931440.23521346149097
4.1888-5.27540.2441520.20381317146998
5.2754-39.25920.2861600.25031391155196
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.70354.7742-4.52565.505-4.42154.03340.10570.0594-0.4221-0.17290.0670.42640.5199-0.79890.66591.4824-0.2964-0.95931.7136-0.83041.5847-28.79121.605-3.2648
29.96514.2438-3.8921.8336-1.68591.5445-0.4098-1.5841.49221.19770.1393-0.0056-1.8563-0.22060.43511.01510.2186-0.240.5401-0.08690.4046-37.6128-9.4057-4.0906
30.02050.01840.43954.8839-2.39425.6843-0.06991.44650.363-0.5876-1.225-0.92180.97161.6643-0.27410.66750.1941-0.36080.74460.06030.2428-24.7017-25.0226-5.5665
45.8451-1.51443.71056.59340.00515.79830.07031.0301-0.0351-1.0253-0.12230.10820.39910.463-0.02110.83370.0859-0.14090.5988-0.00610.5678-29.5143-25.5386-11.2663
56.8752-1.83752.87788.2059-0.71572.0975-1.0964-1.1766-0.13231.09530.72890.2533-0.71350.41340.17410.60520.1153-0.16770.9765-0.0640.5663-26.8437-22.89722.2458
61.87470.96290.98245.4878-1.42582.3589-0.7633-0.7901-0.12150.16780.97731.450.39470.0952-0.00280.95050.4025-0.02260.73520.01380.671-34.8282-27.2217-0.5685
77.88220.9234-1.72231.7995-3.72967.6834-0.5112-0.5692-0.0685-1.0146-0.95292.24560.6297-1.58770.48060.7917-0.0349-0.31191.0075-0.40721.2468-41.4048-30.1204-7.8448
89.29253.9345-1.94498.3642-8.07562.0351-1.69770.11232.3092-1.2025-0.54130.0906-2.42911.7156-2.13421.3603-0.1402-0.381.0525-0.1570.4764-29.0747-10.9933.2196
92.98621.23294.34724.21040.37496.861-0.6696-0.04750.79840.3808-0.8811-0.0014-1.8769-1.6423-2.4741.17990.2723-0.56610.5002-0.12420.6432-23.1925-10.15-4.3791
103.6291-0.62833.94422.5387-0.37696.9991-0.2110.5626-0.2572-0.2592-0.1979-0.47420.60560.76510.32470.84280.12710.03830.56430.05370.8644-29.4691-9.1203-23.0729
118.0151-4.49113.95697.0669-0.7535.4798-0.1829-0.3339-1.1605-0.71070.2665-0.79970.27440.4635-0.0430.78350.12370.13720.6764-0.01630.665-30.1361-9.9248-15.0765
124.33990.07770.16985.4148-0.02018.5799-0.5856-0.75110.9870.89420.11060.3746-1.7243-0.80380.47330.83430.0808-0.09780.608-0.15190.5867-33.28250.9877-14.2062
137.4858-0.0717-1.7643.6764-2.20886.26080.0733-1.1939-0.49991.9250.0385-0.95290.09272.0206-0.04640.82310.0284-0.27260.64490.09590.7826-24.19530.2829-17.7726
145.87550.8457-0.42467.9157-1.41065.00910.69890.32410.0577-0.2548-0.1999-1.88340.54632.8379-0.57330.61110.08980.02951.34660.08071.3017-16.7287-5.1893-22.4794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resseq 54:58)B54 - 58
2X-RAY DIFFRACTION2chain 'B' and (resseq 59:71)B59 - 71
3X-RAY DIFFRACTION3chain 'B' and (resseq 72:82)B72 - 82
4X-RAY DIFFRACTION4chain 'B' and (resseq 83:112)B83 - 112
5X-RAY DIFFRACTION5chain 'B' and (resseq 113:132)B113 - 132
6X-RAY DIFFRACTION6chain 'B' and (resseq 133:145)B133 - 145
7X-RAY DIFFRACTION7chain 'B' and (resseq 146:156)B146 - 156
8X-RAY DIFFRACTION8chain 'A' and (resseq 54:63)A54 - 63
9X-RAY DIFFRACTION9chain 'A' and (resseq 64:71)A64 - 71
10X-RAY DIFFRACTION10chain 'A' and (resseq 72:99)A72 - 99
11X-RAY DIFFRACTION11chain 'A' and (resseq 100:112)A100 - 112
12X-RAY DIFFRACTION12chain 'A' and (resseq 113:132)A113 - 132
13X-RAY DIFFRACTION13chain 'A' and (resseq 133:145)A133 - 145
14X-RAY DIFFRACTION14chain 'A' and (resseq 146:156)A146 - 156

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