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

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Basic information

Entry
Database: PDB / ID: 7fsu
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z729726784
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 / 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 / syndecan binding / neurexin family protein 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 / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ionotropic glutamate receptor binding / ephrin receptor binding / protein sequestering activity / 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 / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / 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 / 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 / Chem-YDU / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.97 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)87,25121
Polymers85,7244
Non-polymers1,52717
Water6,215345
1
A: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4932
Polymers21,4311
Non-polymers621
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)22,36410
Polymers21,4311
Non-polymers9339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.951, 49.447, 114.739
Angle α, β, γ (deg.)90.000, 94.960, 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, 362 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


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


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-YDU / 2-cyclopentyl-N-(3-methyl-1,2,4-oxadiazol-5-yl)acetamide


Mass: 209.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-ALA / ALANINE / Alanine


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


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.67 Å3/Da / Density % sol: 53.91 % / Mosaicity: 0 °
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: 1.97→114.3 Å / Num. obs: 64274 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.976 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.077 / Rrim(I) all: 0.145 / Net I/σ(I): 10.4 / Num. measured all: 223464 / Scaling rejects: 0
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
1.97-2.023.61.5661674746750.2830.9661.8440.898.5
8.82-114.33.10.07124547960.9320.0440.08456.999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BLU

8blu


Resolution: 1.97→114.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.759 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 3118 4.9 %RANDOM
Rwork0.2003 ---
obs0.2026 61080 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 216.94 Å2 / Biso mean: 44.376 Å2 / Biso min: 22.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20.89 Å2
2--0.21 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.97→114.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 98 347 6353
Biso mean--57.48 45.42 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0148059
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157144
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.6439820
X-RAY DIFFRACTIONr_angle_other_deg1.3161.60116543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9785962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04723.412340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3061538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021618
X-RAY DIFFRACTIONr_mcbond_it2.1133.6114079
X-RAY DIFFRACTIONr_mcbond_other2.1393.5633976
X-RAY DIFFRACTIONr_mcangle_it3.4625.2254678
LS refinement shellResolution: 1.971→2.023 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 214 -
Rwork0.385 4390 -
all-4604 -
obs--97.38 %
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)
11.6481-0.1218-0.77680.03620.14210.65430.0716-0.0465-0.2405-0.0418-0.0533-0.007-0.1633-0.1136-0.01840.06010.05120.05050.12560.01110.1598-29.2573.151-45.407
20.64720.1254-0.11610.2845-0.52761.0541-0.03450.147-0.18240.0683-0.0281-0.0951-0.15410.05350.06260.0281-0.01840.01890.0604-0.00620.203-46.398-14.761-13.018
30.78760.1299-0.25440.30170.54671.31930.0583-0.045-0.1028-0.02790.0031-0.0611-0.09810.0303-0.06140.01470.00190.02220.06490.00080.1413-3.2052.127-51.009
40.32370.1081-0.16530.3703-0.41030.5360.05580.0673-0.01860.0707-0.03330.0591-0.0320.0389-0.02250.0610.0060.04880.0308-0.01610.15469.174-13.871-5.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 298
2X-RAY DIFFRACTION2B106 - 298
3X-RAY DIFFRACTION3C106 - 298
4X-RAY DIFFRACTION4D108 - 298
5X-RAY DIFFRACTION4D301

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