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- PDB-2pwq: Crystal structure of a putative ubiquitin conjugating enzyme from... -

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Basic information

Entry
Database: PDB / ID: 2pwq
TitleCrystal structure of a putative ubiquitin conjugating enzyme from Plasmodium yoelii
ComponentsUbiquitin conjugating enzyme
KeywordsLIGASE / Ubiquitin conjugating enzyme / Plasmodium yoelii / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / mitochondrion / ATP binding
Similarity search - Function
UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesPlasmodium yoelii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQiu, W. / Dong, A. / Hassanali, A. / Lin, L. / Brokx, S. / Altamentova, S. / Hills, T. / Lew, J. / Ravichandran, M. / Kozieradzki, I. ...Qiu, W. / Dong, A. / Hassanali, A. / Lin, L. / Brokx, S. / Altamentova, S. / Hills, T. / Lew, J. / Ravichandran, M. / Kozieradzki, I. / Zhao, Y. / Schapira, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of a putative ubiquitin conjugating enzyme from Plasmodium yoelii.
Authors: Qiu, W. / Dong, A. / Hassanali, A. / Lin, L. / Brokx, S. / Altamentova, S. / Hills, T. / Lew, J. / Ravichandran, M. / Kozieradzki, I. / Zhao, Y. / Schapira, M. / Edwards, A.M. / Arrowsmith, ...Authors: Qiu, W. / Dong, A. / Hassanali, A. / Lin, L. / Brokx, S. / Altamentova, S. / Hills, T. / Lew, J. / Ravichandran, M. / Kozieradzki, I. / Zhao, Y. / Schapira, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)24,4931
Polymers24,4931
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.556, 48.556, 179.502
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ubiquitin conjugating enzyme


Mass: 24492.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Strain: 17XNL / Gene: PY01609 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-Rosetta Oxford / References: UniProt: Q7RP52
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M Sodium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 5, 2007 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 20286 / Num. obs: 19987 / % possible obs: 98.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.037 / Net I/σ(I): 59.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 877 / Rsym value: 0.664 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F4Z

2f4z


Resolution: 1.9→24.27 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.921 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30767 1014 5.1 %RANDOM
Rwork0.26747 ---
obs0.26941 18856 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.658 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 0 64 1314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221289
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9531761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81625.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.032152
X-RAY DIFFRACTIONr_chiral_restr0.1170.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02993
X-RAY DIFFRACTIONr_nbd_refined0.2050.2617
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.23
X-RAY DIFFRACTIONr_mcbond_it1.6051.5796
X-RAY DIFFRACTIONr_mcangle_it2.61921283
X-RAY DIFFRACTIONr_scbond_it3.7743556
X-RAY DIFFRACTIONr_scangle_it5.2984.5476
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 82 -
Rwork0.419 1194 -
obs--87.82 %

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