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- PDB-3vqf: Crystal Structure Analysis of the PDZ Domain Derived from the Tig... -

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Basic information

Entry
Database: PDB / ID: 3vqf
TitleCrystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein
ComponentsE3 ubiquitin-protein ligase LNX
KeywordsPEPTIDE BINDING PROTEIN / PDZ domain / claudin C-terminus
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / PDZ domain binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / 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 ...Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase LNX
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsAkiyoshi, Y. / Hamada, D. / Goda, N. / Tenno, T. / Narita, H. / Nakagawa, A. / Furuse, M. / Suzuki, M. / Hiroaki, H.
CitationJournal: To be Published
Title: Structural basis for down regulation of tight junction by PDZ-domain containing E3-Ubiquitin ligase
Authors: Akiyoshi, Y. / Nakakura, Y. / Hamada, D. / Goda, N. / Tenno, T. / Narita, H. / Nakagawa, A. / Furuse, M. / Suzuki, M. / Hiroaki, H.
History
DepositionMar 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase LNX


Theoretical massNumber of molelcules
Total (without water)10,3871
Polymers10,3871
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.493, 51.210, 33.291
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21A-275-

HOH

31A-277-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase LNX


Mass: 10386.552 Da / Num. of mol.: 1 / Fragment: second PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lnx1 / Plasmid: pGEX-6P3-PRESAT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O70263
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 23% PEG 8000, 0.2M sodium acetate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.199→30 Å / Num. all: 27352 / Num. obs: 27350 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 10.91 Å2 / Rmerge(I) obs: 0.062
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.2-1.227.20.1845.11332198.4
1.22-1.247.30.24.91371197.6
1.24-1.277.30.2084.91329198.7
1.27-1.2980.2424.71338197.8
1.29-1.32140.2493.41380199
1.32-1.3514.70.2893.31333198.3
1.35-1.3914.60.3183.21368198.8
1.39-1.4214.80.3733.21365199.1
1.42-1.4614.70.4433.21369199.1
1.46-1.5114.80.5463.21363199.3
1.51-1.5714.80.663.31365199.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vwr

2vwr


Resolution: 1.199→26.195 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9279 / SU ML: 0.11 / σ(F): 0 / Phase error: 13.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 1396 5.1 %RANDOM
Rwork0.1447 ---
obs0.1457 27350 99 %-
all-27352 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.603 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 47.68 Å2 / Biso mean: 15.669 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.0773 Å2-0 Å20.4067 Å2
2---0.5969 Å2-0 Å2
3---0.6742 Å2
Refinement stepCycle: LAST / Resolution: 1.199→26.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 181 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006734
X-RAY DIFFRACTIONf_angle_d1.0871005
X-RAY DIFFRACTIONf_chiral_restr0.075112
X-RAY DIFFRACTIONf_plane_restr0.005138
X-RAY DIFFRACTIONf_dihedral_angle_d12.444293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1986-1.24140.16311310.15992525265697
1.2414-1.29110.20341430.14982541268498
1.2911-1.34990.17681230.1382589271299
1.3499-1.4210.14991290.12512613274299
1.421-1.510.1521440.11862583272799
1.51-1.62660.1531490.117726012750100
1.6266-1.79030.18381380.134626102748100
1.7903-2.04920.17681370.147126342771100
2.0492-2.58150.16851470.149426212768100
2.5815-26.2010.15251550.15482637279299

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