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- PDB-5din: Structural Basis for the Indispensable Role of a Unique Zinc Fing... -

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Basic information

Entry
Database: PDB / ID: 5din
TitleStructural Basis for the Indispensable Role of a Unique Zinc Finger Motif in LNX2 Ubiquitination
ComponentsLigand of Numb protein X 2
KeywordsLIGASE / E3 ligase / Ubiquitination
Function / homology
Function and homology information


neural precursor cell proliferation / PDZ domain binding / neuron differentiation / ubiquitin-protein transferase activity / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
: / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ligand of Numb protein X 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.864 Å
AuthorsSivaraman, J. / Nayak, D.
CitationJournal: Oncotarget / Year: 2015
Title: Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination.
Authors: Nayak, D. / Sivaraman, J.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ligand of Numb protein X 2
B: Ligand of Numb protein X 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,40211
Polymers30,6842
Non-polymers7199
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-8 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.969, 69.399, 52.249
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ligand of Numb protein X 2 / Numb-binding protein 2 / PDZ domain-containing RING finger protein 1


Mass: 15341.971 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX2, PDZRN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N448, ubiquitin-protein ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate, 12% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.864→24.24 Å / Num. obs: 25094 / % possible obs: 98.92 % / Redundancy: 7.2 % / Rsym value: 0.1 / Net I/σ(I): 9.91

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.864→24.24 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 3881 7.92 %Random selection
Rwork0.1899 ---
obs0.1933 25094 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.864→24.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 20 243 2260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012090
X-RAY DIFFRACTIONf_angle_d1.0912825
X-RAY DIFFRACTIONf_dihedral_angle_d14.467789
X-RAY DIFFRACTIONf_chiral_restr0.073300
X-RAY DIFFRACTIONf_plane_restr0.006355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8637-1.88640.24791070.2371443X-RAY DIFFRACTION88
1.8864-1.91030.30081530.22321517X-RAY DIFFRACTION94
1.9103-1.93540.25771250.20711562X-RAY DIFFRACTION94
1.9354-1.96190.2551270.21861558X-RAY DIFFRACTION96
1.9619-1.98990.24911440.19541590X-RAY DIFFRACTION97
1.9899-2.01960.24261310.19711596X-RAY DIFFRACTION97
2.0196-2.05120.27511490.19191618X-RAY DIFFRACTION99
2.0512-2.08480.26771270.19671598X-RAY DIFFRACTION99
2.0848-2.12070.24781440.18941630X-RAY DIFFRACTION99
2.1207-2.15920.24111350.19441622X-RAY DIFFRACTION100
2.1592-2.20070.28741410.20131652X-RAY DIFFRACTION100
2.2007-2.24560.24141320.18621632X-RAY DIFFRACTION100
2.2456-2.29440.28961430.19681604X-RAY DIFFRACTION100
2.2944-2.34770.21271480.20211650X-RAY DIFFRACTION100
2.3477-2.40640.29431320.19651619X-RAY DIFFRACTION100
2.4064-2.47140.24291340.20781665X-RAY DIFFRACTION100
2.4714-2.54410.26711420.20491623X-RAY DIFFRACTION100
2.5441-2.62610.26131490.20961629X-RAY DIFFRACTION100
2.6261-2.71980.23281400.18821640X-RAY DIFFRACTION100
2.7198-2.82860.22931360.20351581X-RAY DIFFRACTION100
2.8286-2.95710.21391400.19281666X-RAY DIFFRACTION100
2.9571-3.11270.21111500.19591644X-RAY DIFFRACTION100
3.1127-3.30730.26761460.21851630X-RAY DIFFRACTION100
3.3073-3.56190.21691390.18621613X-RAY DIFFRACTION100
3.5619-3.9190.19151430.1651630X-RAY DIFFRACTION99
3.919-4.4830.20431410.15141629X-RAY DIFFRACTION100
4.483-5.63630.2021420.16751629X-RAY DIFFRACTION100
5.6363-24.2420.20741410.19081641X-RAY DIFFRACTION100

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