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- PDB-1z2u: The 1.1A crystallographic structure of ubiquitin-conjugating enzy... -

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Basic information

Entry
Database: PDB / ID: 1z2u
TitleThe 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance
ComponentsUbiquitin-conjugating enzyme E2 2
KeywordsLIGASE / PSI / SECSG / ubiquitin-conjugating enzyme / Caenorhabditis elegans / proteosome pathway / Structural Genomics / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics
Function / homology
Function and homology information


Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Signaling by BMP / Downregulation of SMAD2/3:SMAD4 transcriptional activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme ...Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Signaling by BMP / Downregulation of SMAD2/3:SMAD4 transcriptional activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein polyubiquitination / ubiquitin-protein transferase activity / chromosome / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / 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
(R,R)-2,3-BUTANEDIOL / Ubiquitin-conjugating enzyme E2 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsGavira, J.A. / DiGiamamarino, E. / Tempel, W. / Liu, Z.J. / Wang, B.C. / Meehan, E. / Ng, J.D. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance
Authors: Gavira, J.A. / DiGiamamarino, E. / Tempel, W. / Liu, Z.J. / Wang, B.C. / Meehan, E. / Ng, J.D.
History
DepositionMar 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / 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 1.5Aug 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 E2 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,42120
Polymers17,0051
Non-polymers41619
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.604, 60.457, 43.980
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ubiquitin-conjugating enzyme E2 2 / Ubiquitin-protein ligase 2 / Ubiquitin carrier protein 2


Mass: 17005.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ubc-2, let-70 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35129, ubiquitin-protein ligase

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Non-polymers , 5 types, 132 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 277.5 K / Method: capillary counter-diffusion / pH: 5
Details: 7mg/mL protein in 2mM sodium citrate, 10% (v/v) ethanol, 1.5M Sodium Chloride, pH 5.0, capillary counter-diffusion, temperature 277.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 58674 / % possible obs: 97.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Χ2: 0.907
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.1-1.1430.14355410.9492.6
1.14-1.183.70.12857250.92395.3
1.18-1.244.10.11357780.96696.6
1.24-1.34.30.10358080.95796.8
1.3-1.394.40.08758490.97797.4
1.39-1.494.90.08859170.98398.2
1.49-1.647.50.08859360.95698.6
1.64-1.887.60.06559620.94799.2
1.88-2.377.60.05160320.88199.7
2.37-307.40.04661260.69599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005refinement
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1qcq

1qcq


Resolution: 1.1→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.148 / WRfactor Rwork: 0.128 / SU B: 0.6 / SU ML: 0.014 / SU R Cruickshank DPI: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 5900 10.181 %RANDOM
Rwork0.1305 ---
all0.132 ---
obs-57952 96.162 %-
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: 7.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.264 Å20 Å2-0.109 Å2
2--0.037 Å20 Å2
3----0.362 Å2
Refinement stepCycle: LAST / Resolution: 1.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 29 113 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221315
X-RAY DIFFRACTIONr_bond_other_d0.0020.021236
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9781801
X-RAY DIFFRACTIONr_angle_other_deg0.88932891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3775149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.04522.98257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5661510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.2160.2268
X-RAY DIFFRACTIONr_nbd_other0.1840.21229
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2640
X-RAY DIFFRACTIONr_nbtor_other0.0860.2764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.260
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0470.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_mcbond_it1.7242782
X-RAY DIFFRACTIONr_mcbond_other0.8732294
X-RAY DIFFRACTIONr_mcangle_it2.54831315
X-RAY DIFFRACTIONr_mcangle_other1.58831097
X-RAY DIFFRACTIONr_scbond_it2.2922554
X-RAY DIFFRACTIONr_scbond_other1.04121032
X-RAY DIFFRACTIONr_scangle_it3.1513486
X-RAY DIFFRACTIONr_scangle_other1.63931794
X-RAY DIFFRACTIONr_sphericity_free6.8993130
X-RAY DIFFRACTIONr_sphericity_bonded2.91432515
X-RAY DIFFRACTIONr_rigid_bond_restr1.20632662
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 (%)
1.1-1.1280.1574110.1323444444286.785
1.128-1.1590.1333980.1093552428992.096
1.159-1.1920.1344450.1023558425194.166
1.192-1.2290.1193810.0963481408494.564
1.229-1.2690.1274000.0993359394395.334
1.269-1.3140.1293750.0983266380195.791
1.314-1.3630.1273560.1033248374696.209
1.363-1.4190.1353540.1043100357096.751
1.419-1.4820.1253230.1043031343097.784
1.482-1.5540.1393130.1092870324997.969
1.554-1.6380.133090.1092751312098.077
1.638-1.7380.1282850.122632295198.848
1.738-1.8570.142750.1242473277698.991
1.857-2.0060.1532650.1372278256399.22
2.006-2.1970.1512300.132139237799.663
2.197-2.4550.1432200.1421941216599.815
2.455-2.8330.1641890.1551719191299.791
2.833-3.4660.1831810.1611431161399.938
3.466-4.8860.1711170.1591152127199.843
4.886-42.1820.229730.22662771298.315

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