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- PDB-1n99: CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN -

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Basic information

Entry
Database: PDB / ID: 1n99
TitleCRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN
ComponentsSyntenin 1
KeywordsSIGNALING PROTEIN / PDZ domain
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / ionotropic glutamate receptor binding / ephrin receptor binding / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / regulation of mitotic cell cycle / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / blood microparticle / 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 / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / 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 / MAD / Resolution: 1.94 Å
AuthorsKang, B.S. / Cooper, D.R. / Jelen, F. / Devedjiev, Y. / Derewenda, U. / Dauter, Z. / Otlewski, J. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2003
Title: PDZ Tandem of Human Syntenin: Crystal Structure and Functional Properties
Authors: Kang, B.S. / Cooper, D.R. / Jelen, F. / Devedjiev, Y. / Derewenda, U. / Dauter, Z. / Otlewski, J. / Derewenda, Z.S.
History
DepositionNov 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Syntenin 1
B: Syntenin 1


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,4132
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-9 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.727, 48.678, 74.690
Angle α, β, γ (deg.)90.00, 120.82, 90.00
Int Tables number5
Space group name H-MC121
DetailsEach monomer is a biological assembly

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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: 18206.270 Da / Num. of mol.: 2 / Fragment: PDZ Tandem
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP OR MDA9 OR SYCL / Plasmid: pGST-parallel1 / Production host: Escherichia coli (E. coli) / Strain (production host): D834 / References: UniProt: O00560
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: sodium acetate, PEG4000, ammonium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium acetate1reservoirpH4.6
224 %PEG40001reservoir
30.2 Mammonium acetate1reservoir
46 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946, 0.97133, 0.97900
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.971331
30.9791
ReflectionResolution: 1.94→30 Å / Num. obs: 23111 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.29
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2170 / % possible all: 94.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 23095 / % possible obs: 98.8 % / Redundancy: 3.7 % / Num. measured all: 86109 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 90.2 % / Rmerge(I) obs: 0.311

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
SHARPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.308 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1182 5.1 %RANDOM
Rwork0.18424 ---
obs0.18641 21926 99.7 %-
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: 21.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20.62 Å2
2--0.05 Å20 Å2
3---2.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 0 254 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212454
X-RAY DIFFRACTIONr_bond_other_d0.0010.022280
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9453315
X-RAY DIFFRACTIONr_angle_other_deg0.87435303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5425323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02454
X-RAY DIFFRACTIONr_nbd_refined0.2470.3452
X-RAY DIFFRACTIONr_nbd_other0.2670.32743
X-RAY DIFFRACTIONr_nbtor_other0.0940.51630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.526
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.9021.51599
X-RAY DIFFRACTIONr_mcangle_it3.0622575
X-RAY DIFFRACTIONr_scbond_it5.0183855
X-RAY DIFFRACTIONr_scangle_it7.5284.5740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 79
Rwork0.24 1560
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.49011.66650.53314.74880.20661.4838-0.15190.2056-0.1612-0.26710.2494-0.25250.1707-0.0105-0.09740.1062-0.03020.04810.11890.00750.025928.941-13.6979.727
23.6759-0.7084-0.66353.88851.50392.1664-0.02840.2724-0.0987-0.10930.13310.2292-0.00110.0513-0.10470.0389-0.0169-0.00150.08590.02040.06135.7740.312.972
32.14590.3090.04462.07180.91572.1608-0.1679-0.04050.04890.06590.1251-0.1026-0.15620.05910.04290.0837-0.00970.01480.08450.03910.086114.83820.34625.414
42.79310.63510.09262.73380.21811.37530.0748-0.02630.38320.1843-0.0488-0.10480.10730.0388-0.02610.0346-0.01620.03430.0374-0.01860.147638.6127.45719.571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA112 - 1945 - 87
2X-RAY DIFFRACTION2AA197 - 27190 - 164
3X-RAY DIFFRACTION3BB112 - 1945 - 87
4X-RAY DIFFRACTION4BB197 - 27090 - 163
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8
LS refinement shell
*PLUS
Rfactor Rwork: 0.24

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