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- PDB-3kfv: Crystal structure of the SH3-kinase fragment of tight junction pr... -

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Basic information

Entry
Database: PDB / ID: 3kfv
TitleCrystal structure of the SH3-kinase fragment of tight junction protein 3 (TJP3) in apo-form
ComponentsTight junction protein ZO-3
KeywordsCELL ADHESION / Structural genomics consortium / SGC / Cell junction / Cell membrane / Membrane / SH3 domain / Tight junction
Function / homology
Function and homology information


maintenance of blood-brain barrier / bicellular tight junction / cell junction / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Tight junction protein ZO-3 / Tight junction protein ZO / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / PDZ domain ...Tight junction protein ZO-3 / Tight junction protein ZO / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tight junction protein ZO-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.8 Å
AuthorsTong, Y. / Nedyalkova, L. / Tempel, W. / Zhong, N. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / Nedyalkova, L. / Tempel, W. / Zhong, N. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the SH3-kinase fragment of tight junction protein 3 (TJP3) in apo-form
Authors: Tong, Y. / Nedyalkova, L. / Tempel, W. / Zhong, N. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tight junction protein ZO-3


Theoretical massNumber of molelcules
Total (without water)35,18111
Polymers35,1811
Non-polymers010
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.654, 88.654, 92.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Tight junction protein ZO-3 / / Zonula occludens protein 3 / Zona occludens protein 3 / Tight junction protein 3


Mass: 35181.371 Da / Num. of mol.: 1
Fragment: SH3 and Guanylate kinase-like domain residues 489-789
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TJP3, ZO3
Plasmid details: pET28a-LIC-CHis (NCBI GI:145307000) Digested with NcoI and BseRI
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95049
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically

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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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% MPD, 1.4M ammonium sulfate, 0.1M HEPES, 0.01M ADP, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9570 / % possible obs: 99.1 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.155 / Χ2: 1.236 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-3.028.40.83417740.96295.3
3.02-3.3213.70.46919090.989100
3.32-3.814.50.21318841.099100
3.8-4.7914.30.11119351.38100
4.79-5013.40.07120681.6100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
SADABSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.327 Å / FOM work R set: 0.781 / Stereochemistry target values: ML
Details: The programs ARP/WARP (map improvement mode), BUCCANEER, COOT, MOLPROBITY were also used during refinement.
RfactorNum. reflection% reflection
Rfree0.29 449 4.71 %
Rwork0.222 --
obs0.225 9536 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.639 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 93.72 Å2 / Biso mean: 45.35 Å2 / Biso min: 24.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.574 Å20 Å2-0 Å2
2--4.574 Å20 Å2
3----9.147 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 10 0 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051921
X-RAY DIFFRACTIONf_angle_d0.7942616
X-RAY DIFFRACTIONf_chiral_restr0.052302
X-RAY DIFFRACTIONf_plane_restr0.005335
X-RAY DIFFRACTIONf_dihedral_angle_d15.255691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-3.2050.331470.2712929307699
3.205-4.0380.261540.19129823136100
4.038-44.3330.2961480.2231763324100

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