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- PDB-1r6j: Ultrahigh resolution Crystal Structure of syntenin PDZ2 -

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Basic information

Entry
Database: PDB / ID: 1r6j
TitleUltrahigh resolution Crystal Structure of syntenin PDZ2
ComponentsSyntenin 1
KeywordsMEMBRANE PROTEIN / PDZ
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / syndecan binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / neurexin family protein binding / syndecan binding / Neurofascin interactions / presynapse assembly / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of mitotic cell cycle / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / cell adhesion molecule binding / ephrin receptor binding / protein sequestering activity / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / extracellular vesicle / azurophil granule lumen / melanosome / presynapse / chemical synaptic transmission / actin cytoskeleton organization / positive regulation of cell growth / blood microparticle / nuclear membrane / Ras protein signal transduction / cytoskeleton / positive regulation of cell migration / intracellular signal transduction / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.73 Å
AuthorsKang, B.S. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between small molecule and macromolecular crystal chemistry
Authors: Kang, B.S. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Syntenin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7452
Polymers8,7101
Non-polymers351
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.876, 39.544, 32.276
Angle α, β, γ (deg.)90.00, 109.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Syntenin 1 / Syndecan binding protein 1 / Melanoma differentiation associated protein-9 / Mda-9 / Scaffold ...Syndecan binding protein 1 / Melanoma differentiation associated protein-9 / Mda-9 / Scaffold protein Pbp1 / Pro-TGF-alpha cytoplasmic domain-interacting protein 18 / TACIP18


Mass: 8709.964 Da / Num. of mol.: 1 / Fragment: PDZ2 domain (residues 197-273)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP OR MDA9 OR SYCL / Plasmid: pGST-parallel1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O00560
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.79 Å3/Da / Density % sol: 31.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.85 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.73→20 Å / Num. obs: 71347 / % possible obs: 83.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 3.8 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 0.73→0.76 Å / Rmerge(I) obs: 0.387 / % possible all: 9.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.73→10 Å / Num. parameters: 9304 / Num. restraintsaints: 610 / Cross valid method: FREE R
Details: Rwork and Rfree are the values before the final refinement including Free reflections
RfactorNum. reflection% reflectionSelection details
Rfree0.0866 1389 -RANDOM
Rwork0.0747 ---
obs-71289 84.4 %-
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 604.03 / Occupancy sum non hydrogen: 757.02
Refinement stepCycle: LAST / Resolution: 0.73→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 0 1 237 964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0355
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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