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- PDB-2h2y: Crystal structure of ubiquitin conjugating enzyme E2 from plasmod... -

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Basic information

Entry
Database: PDB / ID: 2h2y
TitleCrystal structure of ubiquitin conjugating enzyme E2 from plasmodium falciparum
ComponentsUbiquitin-conjugating enzyme
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ISG15 antiviral mechanism / ubiquitin-protein ligase / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / regulation of cell cycle process / apicoplast / ubiquitin conjugating enzyme activity / ligase activity / : / protein polyubiquitination ...ISG15 antiviral mechanism / ubiquitin-protein ligase / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / regulation of cell cycle process / apicoplast / ubiquitin conjugating enzyme activity / ligase activity / : / protein polyubiquitination / ubiquitin-protein transferase activity / membrane => GO:0016020 / protein ubiquitination / ATP hydrolysis activity / nucleus
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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
Ubiquitin-conjugating enzyme E2
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsQiu, W. / Dong, A. / Zhao, Y. / Lew, J. / Kozieradski, I. / Sundararajan, E. / Melone, M. / Wasney, G. / Vedadi, M. / Edwards, A.M. ...Qiu, W. / Dong, A. / Zhao, Y. / Lew, J. / Kozieradski, I. / Sundararajan, E. / Melone, M. / Wasney, G. / Vedadi, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / 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
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: 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
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
A: Ubiquitin-conjugating enzyme
B: Ubiquitin-conjugating enzyme
C: Ubiquitin-conjugating enzyme
D: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)62,3644
Polymers62,3644
Non-polymers00
Water27015
1
A: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)15,5911
Polymers15,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)15,5911
Polymers15,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)15,5911
Polymers15,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)15,5911
Polymers15,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.117, 85.414, 93.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer.

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Components

#1: Protein
Ubiquitin-conjugating enzyme /


Mass: 15591.063 Da / Num. of mol.: 4 / Fragment: Residue 115-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Species: Plasmodium falciparum / Strain: isolate 3D7 / Gene: MAL13P1.227 / Plasmid: pET15-tev-lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDP1, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.4
Details: 29% Peg 3350, 0.1M (NH4)2SO4, 0.1M Bis-Tris, 5% Glycerol, pH 6.4, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 13587 / Num. obs: 13521 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.082 / Net I/σ(I): 38.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.1 % / Num. unique all: 1334 / Rsym value: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FO3

2fo3


Resolution: 2.8→34.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 989 -RANDOM
Rwork0.232 ---
all0.229 13504 --
obs0.282 13245 98.1 %-
Displacement parametersBiso mean: 22.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 0 15 3807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.347 156 -
Rwork0.318 --
obs-2098 95.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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