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- PDB-2ayv: Crystal structure of a putative ubiquitin-conjugating enzyme E2 f... -

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Basic information

Entry
Database: PDB / ID: 2ayv
TitleCrystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii
Componentsubiquitin-conjugating enzyme E2
KeywordsLIGASE / Structural Genomics / Structural Genomics Consortium / ubiquitin / ubiquitin-conjugating enzyme / SGC
Function / homologyUbiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsTempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Arrowsmith, C. ...Tempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Bochkarev, A. / Hui, R. / Amani, M. / 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
DepositionSep 8, 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: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 7.37 (7.62 B<40) BAD ROTAMERS : 3.4% 4/119 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/146 (TARGET 0.2%) RAMACHANDRAN FAVORED : 97.3% 142/146 (TARGET 98.0%)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin-conjugating enzyme E2


Theoretical massNumber of molelcules
Total (without water)18,81511
Polymers18,8151
Non-polymers010
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.553, 85.611, 89.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ubiquitin-conjugating enzyme E2


Mass: 18815.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: p15TvL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: ubiquitin-protein ligase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 12360 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.038 / Χ2: 1.021
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2-2.1596.25.40.33123511.11
2.15-2.3799.95.70.19524441.051
2.37-2.711005.80.09224670.9921
2.71-3.421005.90.04124941.0351
3.42-2099.95.80.02526040.9411

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.45 / Cor.coef. Fo:Fc: 0.578
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X23

1x23


Resolution: 2.001→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.26 / SU B: 12.897 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.258 597 4.83 %RANDOM
Rwork0.2261 ---
all0.228 ---
obs-12359 99.333 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.822 Å2
Baniso -1Baniso -2Baniso -3
1-1.984 Å20 Å20 Å2
2--0.39 Å20 Å2
3----2.374 Å2
Refinement stepCycle: LAST / Resolution: 2.001→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 10 16 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221176
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9521614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31924.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.024153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02932
X-RAY DIFFRACTIONr_nbd_refined0.1810.2528
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.22
X-RAY DIFFRACTIONr_mcbond_it2.4532768
X-RAY DIFFRACTIONr_mcangle_it3.30331216
X-RAY DIFFRACTIONr_scbond_it2.8692477
X-RAY DIFFRACTIONr_scangle_it3.6663398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.001-2.0520.434380.32778088192.849
2.052-2.1080.366440.29482488098.636
2.108-2.1680.252530.28478984599.645
2.168-2.2340.374370.25679983899.761
2.234-2.3060.27380.246766804100
2.306-2.3860.258380.264747785100
2.386-2.4750.337330.242706739100
2.475-2.5740.376350.247696731100
2.574-2.6870.245340.239665699100
2.687-2.8150.22250.254646671100
2.815-2.9640.229260.246608634100
2.964-3.140.306320.247583615100
3.14-3.3510.283310.236537568100
3.351-3.6110.255230.223522545100
3.611-3.9430.269310.19745949199.796
3.943-4.3870.244210.182443464100
4.387-5.0250.165150.181388403100
5.025-6.060.244260.235336362100
6.06-8.2020.194110.234279290100
8.202-200.19360.18718919798.985
Refinement TLS params.Method: refined / Origin x: 21.7452 Å / Origin y: 69.7416 Å / Origin z: 76.6636 Å
111213212223313233
T-0.1077 Å2-0.1219 Å20.0981 Å2--0.1769 Å2-0.1497 Å2---0.183 Å2
L4.1505 °2-2.1059 °2-2.2984 °2-4.1878 °24.0579 °2--5.2692 °2
S-0.4043 Å °0.4837 Å °-0.5425 Å °0.1864 Å °-0.3192 Å °0.6788 Å °0.3349 Å °-0.7749 Å °0.7234 Å °
Refinement TLS groupSelection: ALL

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