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- PDB-2av4: Crystal structure of Plasmodium yoelii thioredoxin-like protein 4... -

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Basic information

Entry
Database: PDB / ID: 2av4
TitleCrystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1)
ComponentsThioredoxin-like protein 4A (DIM1)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / thioredoxin-like protein / DIM1 / U5 snRNP-specific 15kD protein / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome
Similarity search - Function
Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Drosophila melanogaster RE13747p
Similarity search - Component
Biological speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsDong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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
Remark 300BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. ...BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 1 chain. The biological unit of the protein is not known.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-like protein 4A (DIM1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8385
Polymers18,6961
Non-polymers1424
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Thioredoxin-like protein 4A (DIM1)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)113,02930
Polymers112,1786
Non-polymers85124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area10560 Å2
ΔGint-327 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.877, 109.877, 85.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1067-

HOH

21A-1199-

HOH

31A-1200-

HOH

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Components

#1: Protein Thioredoxin-like protein 4A (DIM1) / Drosophila melanogaster RE13747p


Mass: 18696.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Gene: PY07357 / Plasmid: pET28aLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q7R866
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 295 K
Details: 1.4 M NaCl, pH 9.0, VAPOR DIFFUSION, temperature 295 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.99998
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.73→41.5 Å / Num. all: 20820 / Num. obs: 20820 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.3
Reflection shellResolution: 1.73→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.28 / Rsym value: 0.385 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGV

1qgv


Resolution: 1.73→41.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.783 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26115 666 3.2 %RANDOM
Rwork0.20798 ---
obs0.20958 19895 98.77 %-
all-19950 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.73→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 4 199 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9381541
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61124.67762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69515201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.447156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02877
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2772
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73521090
X-RAY DIFFRACTIONr_scbond_it2.7533514
X-RAY DIFFRACTIONr_scangle_it4.3084.5451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.728→1.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 46 -
Rwork0.373 1447 -
obs--95.95 %

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