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- PDB-1nte: CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN -

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Basic information

Entry
Database: PDB / ID: 1nte
TitleCRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN
ComponentsSyntenin 1
KeywordsSIGNALING PROTEIN / Syntenin / PDZ recognition
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / Ephrin signaling / protein targeting to membrane / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / regulation of mitotic cell cycle / positive regulation of JNK cascade / adherens junction / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / chemical synaptic transmission / Ras protein signal transduction / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / synapse / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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
OXYGEN ATOM / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsKang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2003
Title: Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.
Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2012Group: Database references / Structure summary
Revision 1.4Aug 16, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Syntenin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7262
Polymers8,7101
Non-polymers161
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.292, 42.570, 31.038
Angle α, β, γ (deg.)90.00, 108.71, 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: PDZ 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP OR MDA9 OR SYCL / Plasmid: pGST-parallel / Production host: Escherichia coli (E. coli) / References: UniProt: O00560
#2: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1.41 Å3/Da / Density % sol: 12.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.0
334 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.1→12.16 Å / Num. all: 18559 / Num. obs: 18559 / % possible obs: 73.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.5
Reflection
*PLUS
Lowest resolution: 13 Å / Num. measured all: 58393
Reflection shell
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 1.14 Å / % possible obs: 11 % / Num. unique obs: 275 / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.46

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N99

1n99


Resolution: 1.24→12.16 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.603 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15331 851 5.1 %RANDOM
Rwork0.11325 ---
obs0.11533 15684 93.13 %-
all-16535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.391 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.26 Å2
2---0.18 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.24→12.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 1 175 784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022632
X-RAY DIFFRACTIONr_bond_other_d0.0020.02590
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.944851
X-RAY DIFFRACTIONr_angle_other_deg1.88531384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.398581
X-RAY DIFFRACTIONr_chiral_restr0.1150.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02687
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02112
X-RAY DIFFRACTIONr_nbd_refined0.2460.2115
X-RAY DIFFRACTIONr_nbd_other0.2520.2709
X-RAY DIFFRACTIONr_nbtor_other0.0850.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.253
X-RAY DIFFRACTIONr_mcbond_it1.3121.5406
X-RAY DIFFRACTIONr_mcangle_it1.9562665
X-RAY DIFFRACTIONr_scbond_it2.4743226
X-RAY DIFFRACTIONr_scangle_it3.3724.5186
X-RAY DIFFRACTIONr_rigid_bond_restr1.2712632
X-RAY DIFFRACTIONr_sphericity_free5.0892176
X-RAY DIFFRACTIONr_sphericity_bonded3.2222625
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.197 38
Rwork0.159 801
Refinement
*PLUS
Rfactor Rfree: 0.153 / Rfactor Rwork: 0.113
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.63

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