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- PDB-3e95: Crystal Structure of the Plasmodium Falciparum ubiquitin conjugat... -

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Basic information

Entry
Database: PDB / ID: 3.0E+95
TitleCrystal Structure of the Plasmodium Falciparum ubiquitin conjugating enzyme complex, PfUBC13-PfUev1a
Components
  • Ubiquitin carrier protein
  • Ubiquitin-conjugating enzyme E2
KeywordsLIGASE / malaria ubiquitin complex structural genomics / Ubl conjugation pathway / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ubiquitin-protein ligase / Aggrephagy / Antigen processing: Ubiquitination & Proteasome degradation / postreplication repair / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / ligase activity / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / ATP binding / nucleus
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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, putative / Ubiquitin-conjugating enzyme E2 N, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Lam, A. / Ali, A. / Brokx, S. / Lin, Y.H. / Zhao, Y. / Lew, J. / Ravichandran, M. / Wasney, G. / Vedadi, M. ...Wernimont, A.K. / Lam, A. / Ali, A. / Brokx, S. / Lin, Y.H. / Zhao, Y. / Lew, J. / Ravichandran, M. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Wilkstrom, M. / BOuntra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Qiu, W. / Brand, V.B. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Plasmodium Falciparum ubiquitin conjugating enzyme complex, PfUBC13-PfUev1a
Authors: Wernimont, A.K. / Lam, A. / Ali, A. / Brokx, S. / Lin, Y.H. / Zhao, Y. / Lew, J. / Ravichandran, M. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Wilkstrom, M. ...Authors: Wernimont, A.K. / Lam, A. / Ali, A. / Brokx, S. / Lin, Y.H. / Zhao, Y. / Lew, J. / Ravichandran, M. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Schapira, M. / Bochkarev, A. / Wilkstrom, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Qiu, W. / Brand, V.B.
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carrier protein
B: Ubiquitin carrier protein
C: Ubiquitin-conjugating enzyme E2


Theoretical massNumber of molelcules
Total (without water)52,6718
Polymers52,6713
Non-polymers05
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-12 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.856, 154.856, 81.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / Refine code: 5

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROAA116 - 118116 - 118
2ASPBB116 - 120116 - 120

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Components

#1: Protein Ubiquitin carrier protein


Mass: 17271.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFE1350c / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli)
References: UniProt: Q8I3J4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Ubiquitin-conjugating enzyme E2


Mass: 18127.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: MAL3P2.20, PFC0255c / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / References: UniProt: O97241
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Mg Formate 20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 38712 / Num. obs: 38635 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.059 / Χ2: 1.923 / Net I/σ(I): 33.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.05 / Num. unique all: 3802 / Χ2: 1.755 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å44.66 Å
Translation2.8 Å44.66 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.782 / SU B: 8.087 / SU ML: 0.178 / SU R Cruickshank DPI: 0.253 / SU Rfree: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1930 5 %RANDOM
Rwork0.248 ---
all0.249 38587 --
obs0.249 38526 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.21 Å2 / Biso mean: 50.613 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20.81 Å20 Å2
2--1.62 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 5 130 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223533
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9764819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.535432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5925.179168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.121518
X-RAY DIFFRACTIONr_chiral_restr0.0560.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022738
X-RAY DIFFRACTIONr_nbd_refined0.160.21522
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.25
X-RAY DIFFRACTIONr_mcbond_it0.3351.52259
X-RAY DIFFRACTIONr_mcangle_it0.60723570
X-RAY DIFFRACTIONr_scbond_it0.44531452
X-RAY DIFFRACTIONr_scangle_it0.7294.51249
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.120.5
LOOSE POSITIONAL0.735
MEDIUM THERMAL0.852
LOOSE THERMAL1.1110
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 142 -
Rwork0.372 2649 -
all-2791 -
obs-2287 99.43 %

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