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- PDB-3cxg: Crystal structure of Plasmodium falciparum thioredoxin, PFI0790w -

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Basic information

Entry
Database: PDB / ID: 3cxg
TitleCrystal structure of Plasmodium falciparum thioredoxin, PFI0790w
ComponentsPutative thioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / malaria / plasmodium / falciparum / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Thioredoxin / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. ...Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / Hui, R. / Hills, T. / Pizarro, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Plasmodium falciparum thioredoxin, PFI0790w.
Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / Hui, R. / Hills, T. / Pizarro, J.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative thioredoxin
B: Putative thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6245
Polymers31,3432
Non-polymers2803
Water2,432135
1
A: Putative thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7642
Polymers15,6721
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8603
Polymers15,6721
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.455, 97.455, 97.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Putative thioredoxin


Mass: 15671.647 Da / Num. of mol.: 2 / Fragment: Residues 18-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFI0790w / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q8I2Z1, UniProt: Q4VWQ3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M Ammonium sulfate, 0.2 M Sodium acetate, 0.1 M Hepes pH 7.5, 5% MPD, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 21155 / Num. obs: 21155 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 30.77 Å2 / Rmerge(I) obs: 0.0507 / Rsym value: 0.0466 / Χ2: 1.225 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 9 % / Rmerge(I) obs: 0.2451 / Mean I/σ(I) obs: 2.09 / Num. unique all: 2073 / Rsym value: 0.4274 / Χ2: 0.976 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.64 Å
Translation2.5 Å23.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.38 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.569 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1089 5.1 %RANDOM
Rwork0.192 ---
obs0.195 21155 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.321 Å2
Refinement stepCycle: LAST / Resolution: 2→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 17 135 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222114
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9312865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98825.913115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33615363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.405152
X-RAY DIFFRACTIONr_chiral_restr0.1520.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021618
X-RAY DIFFRACTIONr_nbd_refined0.2120.2820
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5350.215
X-RAY DIFFRACTIONr_mcbond_it1.2861.51292
X-RAY DIFFRACTIONr_mcangle_it1.70721992
X-RAY DIFFRACTIONr_scbond_it2.9523997
X-RAY DIFFRACTIONr_scangle_it4.1424.5870
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 78 -
Rwork0.248 1460 -
all-1538 -
obs-2086 99.87 %
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)
111.4603-4.9318-0.04357.2-0.62733.48580.42280.2541-0.6999-0.4531-0.00840.56250.3628-0.2447-0.4145-0.0625-0.0406-0.1553-0.08050.10470.011127.84737.85916.316
23.4439-1.93452.53522.443-2.9496.30510.1341-0.1668-0.1651-0.01280.25710.40870.1323-0.6197-0.3912-0.1563-0.02340.0123-0.11070.1148-0.019927.33846.35824.142
32.82-1.48682.0253.3658-2.05593.52660.17410.21470.1049-0.1830.05070.0602-0.10830.1608-0.2248-0.1633-0.01220.0114-0.11520.0661-0.112336.55848.70518.43
47.3149-0.54413.79861.7142-0.8268.39830.0598-0.31280.65490.37950.26890.1733-0.5943-0.7573-0.32870.01460.07790.0996-0.08960.10260.069926.62156.66925.597
510.88950.7427-6.16972.97250.35137.73330.3209-0.93690.37250.3539-0.4575-0.3538-0.34280.64130.1366-0.0619-0.1653-0.06380.04150.12-0.064921.26931.99311.03
62.842.2613-1.65935.2006-2.33282.41690.2062-0.1087-0.13180.1601-0.4344-0.5292-0.03840.42070.2282-0.16270.0055-0.0188-0.01760.1248-0.095821.29624.8952.509
78.40510.90084.61877.4481-4.355111.4796-0.0109-0.12690.25820.2599-0.23720.1102-0.4606-0.12620.2481-0.1897-0.04520.0155-0.15170.0182-0.15317.78927.1047.905
83.28992.2441-1.23945.496-2.0722.51980.03530.3845-0.0044-0.5392-0.1717-0.21190.10840.20580.1364-0.08870.03520.0011-0.02550.0913-0.143817.81527.992-5.919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 349 - 34
2X-RAY DIFFRACTION2AA35 - 7335 - 73
3X-RAY DIFFRACTION3AA74 - 11074 - 110
4X-RAY DIFFRACTION4AA111 - 131111 - 131
5X-RAY DIFFRACTION5BB9 - 339 - 33
6X-RAY DIFFRACTION6BB34 - 7434 - 74
7X-RAY DIFFRACTION7BB75 - 8775 - 87
8X-RAY DIFFRACTION8BB88 - 13188 - 131

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