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- PDB-3we5: Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from A... -

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Basic information

Entry
Database: PDB / ID: 3we5
TitleCrystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita
ComponentsUbiquitin conjugating enzyme
KeywordsLIGASE / alpha / beta / ubiquitin conjugating enzyme E2 / ubiquitin binding
Function / homology
Function and homology information


: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Ubiquitin conjugating enzyme
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, D.F. / Feng, L. / Wang, D.C. / Liu, W.
CitationJournal: To be Published
Title: Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita
Authors: Li, D.F. / Feng, L. / Wang, D.C. / Liu, W.
History
DepositionJul 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4774
Polymers38,3252
Non-polymers1522
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin conjugating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3153
Polymers19,1631
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ubiquitin conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)19,1631
Polymers19,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.930, 34.760, 128.100
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

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Components

#1: Protein Ubiquitin conjugating enzyme / E2 UbcA1


Mass: 19162.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: H9CTH3, ubiquitin-protein ligase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.45 Å / Num. all: 37328 / Num. obs: 37008 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 9.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3958 / Rsym value: 0.204 / % possible all: 72.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FO3

2fo3


Resolution: 1.7→34.641 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 3704 10.01 %RANDOM
Rwork0.2021 ---
all0.2053 37328 --
obs0.2053 37002 93.66 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.318 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0819 Å20 Å2-3.8686 Å2
2--0.2478 Å20 Å2
3----3.3297 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 10 343 2531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082238
X-RAY DIFFRACTIONf_angle_d1.1253040
X-RAY DIFFRACTIONf_dihedral_angle_d14.708822
X-RAY DIFFRACTIONf_chiral_restr0.077338
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72240.3259860.293683562
1.7224-1.7460.3002970.28190167
1.746-1.77090.30431240.2576101874
1.7709-1.79740.3041220.2548105781
1.7974-1.82540.25391240.2408118485
1.8254-1.85540.26211370.2421119590
1.8554-1.88740.28371400.2316127595
1.8874-1.92170.30081830.2688136399
1.9217-1.95860.22971280.22521324100
1.9586-1.99860.24461350.21821405100
1.9986-2.04210.25781310.2021388100
2.0421-2.08960.22891620.20331323100
2.0896-2.14180.23351530.20451354100
2.1418-2.19970.23751310.21311388100
2.1997-2.26440.29781690.2377131899
2.2644-2.33750.22261480.21141371100
2.3375-2.4210.25651440.20691398100
2.421-2.51790.24771660.20381329100
2.5179-2.63250.24211420.19891363100
2.6325-2.77120.24851660.20891354100
2.7712-2.94470.22651580.20511380100
2.9447-3.1720.23271680.20041363100
3.172-3.49090.23611530.18441399100
3.4909-3.99540.19011320.17137399
3.9954-5.03130.18821590.1667136397
5.0313-34.64780.2271460.2082127788

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