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- PDB-7ft4: SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP... -

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Basic information

Entry
Database: PDB / ID: 7ft4
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z48847594
ComponentsSyntenin-1
KeywordsSIGNALING PROTEIN / Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / negative regulation of receptor internalization ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / Neurofascin interactions / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / negative regulation of receptor internalization / positive regulation of exosomal secretion / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / positive regulation of phosphorylation / phosphatidylinositol-4,5-bisphosphate binding / ionotropic glutamate receptor binding / regulation of mitotic cell cycle / protein sequestering activity / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / 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 / protein heterodimerization activity / membrane raft / 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 / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
ALANINE / D-GLUTAMIC ACID / GLYCINE / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.17 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: SDCBP PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Syntenin-1
B: Syntenin-1
C: Syntenin-1
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,17920
Polymers85,7244
Non-polymers1,45516
Water4,900272
1
A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7263
Polymers21,4311
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7024
Polymers21,4311
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6925
Polymers21,4311
Non-polymers2614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0588
Polymers21,4311
Non-polymers6287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.156, 49.086, 115.073
Angle α, β, γ (deg.)90.000, 95.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 21430.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Production host: Escherichia coli (E. coli) / References: UniProt: O00560

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Non-polymers , 7 types, 288 molecules

#2: Chemical ChemComp-O0J / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide


Mass: 233.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.24 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.17→45.12 Å / Num. obs: 39276 / % possible obs: 82.5 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.069 / Rrim(I) all: 0.118 / Net I/σ(I): 6.1 / Num. measured all: 100885 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.17-2.282.51.2141219648020.3620.9031.520.770
6.85-45.122.60.028358513820.9990.0210.03619.887.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0403refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BLU

8blu


Resolution: 2.17→45.16 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.887 / SU B: 17.888 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.443 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3467 1873 4.9 %RANDOM
Rwork0.2486 ---
obs0.2534 36580 80.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.23 Å2 / Biso mean: 52.863 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å20.86 Å2
2---0.75 Å2-0 Å2
3---2.06 Å2
Refinement stepCycle: final / Resolution: 2.17→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 94 272 6274
Biso mean--66.56 44.97 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126141
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166121
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6428252
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5814099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6025776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.12533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.991101168
X-RAY DIFFRACTIONr_chiral_restr0.0640.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
X-RAY DIFFRACTIONr_mcbond_it5.6165.4043113
X-RAY DIFFRACTIONr_mcbond_other5.6115.4043112
X-RAY DIFFRACTIONr_mcangle_it8.4579.6773886
LS refinement shellResolution: 2.167→2.223 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 149 -
Rwork0.405 2814 -
all-2963 -
obs--84.39 %

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