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- PDB-1yf9: Structural analysis of Leishmania major ubiquitin conjugating enz... -

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Basic information

Entry
Database: PDB / ID: 1yf9
TitleStructural analysis of Leishmania major ubiquitin conjugating enzyme E2
ComponentsUbiquitin carrier protein 4
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SGPP / PSI / Protein Structure Initiative / ubiquitin conjugating enzyme / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


ubiquitin-protein ligase / ligase activity / ubiquitin conjugating enzyme activity / protein polyubiquitination / 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 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Putative ubiquitin carrier protein 4
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsStructural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Structural Analysis of Leishmania major ubiquitin conjugating enzyme E2
Authors: Bosch, J. / Hol, W.G.J.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE A database reference sequence for ubiquitin carrier protein 4 can be found at GeneDB, ID LmjF32.0700.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carrier protein 4
B: Ubiquitin carrier protein 4
C: Ubiquitin carrier protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6959
Polymers58,4823
Non-polymers2136
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-71 kcal/mol
Surface area22830 Å2
MethodPISA
2
A: Ubiquitin carrier protein 4
B: Ubiquitin carrier protein 4
C: Ubiquitin carrier protein 4
hetero molecules

A: Ubiquitin carrier protein 4
B: Ubiquitin carrier protein 4
C: Ubiquitin carrier protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,38918
Polymers116,9646
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13860 Å2
ΔGint-160 kcal/mol
Surface area41070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.448, 114.448, 139.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
12B
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNASPASP2AA14 - 8614 - 86
211ASNASNASPASP2BB14 - 8614 - 86
311ASNASNASPASP2CC14 - 8614 - 86
421SERSERPROPRO2AA91 - 17091 - 170
521SERSERPROPRO2BB91 - 17091 - 170
621SERSERPROPRO2CC91 - 17091 - 170
112GLUGLUGLYGLY1BB87 - 9087 - 90
212GLUGLUGLYGLY1CC87 - 9087 - 90

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin carrier protein 4


Mass: 19493.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Description: T7 system / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q4Q5L3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 4.04 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3 M Sodium chloride 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97957, 0.95372, 0.97975
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.953721
30.979751
ReflectionResolution: 2→50 Å / Num. all: 54915 / Num. obs: 54915 / % possible obs: 91.67 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 37.14 Å2 / Rsym value: 0.077 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.108 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 5243 / Rsym value: 0.818 / % possible all: 61.17

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.324 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21039 2919 5 %RANDOM
Rwork0.18486 ---
all0.18613 54915 --
obs0.18613 54915 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.006 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 6 296 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9485682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49523.114228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491542
X-RAY DIFFRACTIONr_chiral_restr0.0880.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023275
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21709
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22812
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.21242504
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93164029
X-RAY DIFFRACTIONr_scbond_it3.00161872
X-RAY DIFFRACTIONr_scangle_it3.937101653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A612tight positional0.050.05
12B612tight positional0.040.05
13C612tight positional0.060.05
21B30tight positional0.030.05
11A586medium positional0.320.5
12B586medium positional0.330.5
13C586medium positional0.350.5
11A612tight thermal0.110.5
12B612tight thermal0.10.5
13C612tight thermal0.110.5
21B30tight thermal0.160.5
11A586medium thermal0.762
12B586medium thermal0.732
13C586medium thermal0.772
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 293 -
Rwork0.258 5243 -
obs--61.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6585-0.42340.86251.3106-0.0041.13950.077-0.26780.08180.16910.0476-0.14580.02150.0486-0.1245-0.2367-0.0161-0.0356-0.0825-0.1148-0.168226.23625.25616.702
26.03951.8502-0.80344.4323-0.15841.99670.0042-0.5143-0.8880.4641-0.072-0.24740.49980.03610.06780.0250.0527-0.046-0.13020.0604-0.065319.583-6.11714.786
32.3213-0.4651-0.26184.52151.23251.5710.0192-0.3621-0.00450.1855-0.11790.06060.1823-0.16820.0987-0.2709-0.0550.05870.0241-0.0604-0.2325-4.40715.53617.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 17013 - 170
2X-RAY DIFFRACTION2BB11 - 17011 - 170
3X-RAY DIFFRACTION3CC13 - 17113 - 171

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