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- PDB-2f4z: Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E... -

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Basic information

Entry
Database: PDB / ID: 2f4z
TitleToxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain
ComponentsTgTwinScan_2721 - E2 domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin conjugating TgTwinScan_2721 / Structural Genomics Consortium / SGC
Function / homologyUbiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsDong, A. / Lew, J. / Zhao, Y. / Melone, M. / Alam, Z. / Kozieradski, I. / Wasney, G. / Vedadi, M. / Sundstrom, M. / Weigelt, J. ...Dong, A. / Lew, J. / Zhao, Y. / Melone, M. / Alam, Z. / Kozieradski, I. / Wasney, G. / Vedadi, M. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Hills, T. / 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
DepositionNov 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Author states that biological unit for the protein is not yet known
Remark 999Sequence No suitable database references were found at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TgTwinScan_2721 - E2 domain
B: TgTwinScan_2721 - E2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1014
Polymers43,0092
Non-polymers922
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.475, 141.334, 77.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-4020-

HOH

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Components

#1: Protein TgTwinScan_2721 - E2 domain


Mass: 21504.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: P28-LIC-THROMBIN DERIVED FROM SOURCE 9 PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.4
Details: 32% Peg 1500, 0.2 M MgCl2, 0.1 M Tris pH 8.4, 10 mM Spermidine, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2005 / Details: VeriMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 23386 / Num. obs: 23386 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 7.6
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.22 / Num. unique all: 1143 / Rsym value: 0.729 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
PHASERV. 1.3.1phasing
Coot0.0.3.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEP

2bep


Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.71 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23779 763 3.3 %RANDOM
Rwork0.1987 ---
all0.19992 22605 --
obs0.19992 22605 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.401 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 7 194 2460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9633175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17624.68194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.115158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021746
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21096
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21562
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3391.51500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13722349
X-RAY DIFFRACTIONr_scbond_it3.2063981
X-RAY DIFFRACTIONr_scangle_it4.9774.5826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.114→2.169 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 68 -
Rwork0.235 1592 -
obs--96.29 %

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