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

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Entry
Database: PDB / ID: 7fsx
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1328078283
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 / 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 / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / 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 / protein sequestering activity / ephrin receptor binding / ionotropic glutamate receptor binding / 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 / 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 / Chem-I8A / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.91 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)87,55823
Polymers85,7244
Non-polymers1,83519
Water7,044391
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)21,9125
Polymers21,4311
Non-polymers4824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9997
Polymers21,4311
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1549
Polymers21,4311
Non-polymers7248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.629, 49.536, 115.265
Angle α, β, γ (deg.)90.000, 95.430, 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, 410 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-I8A / N-(cyclopropylmethyl)-2,2,3,3-tetramethylazetidine-1-carboxamide


Mass: 210.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N2O / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#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.: 391 / 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: 53.99 % / 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: 1.91→114.74 Å / Num. obs: 70825 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.973 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 12.6 / Num. measured all: 246477 / 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
1.91-1.953.61.1921562743840.2560.7431.407197.3
9.16-114.7430.08721847170.8960.0540.10263.899.9

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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: 1.91→114.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.556 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3446 4.9 %RANDOM
Rwork0.1957 ---
obs0.1976 67272 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.5 Å2 / Biso mean: 38.891 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å21.54 Å2
2---0.42 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 1.91→114.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 118 392 6418
Biso mean--52.7 40.82 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0148643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157604
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.65210248
X-RAY DIFFRACTIONr_angle_other_deg1.3361.61217588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.045995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91222.808349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.394151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5411544
X-RAY DIFFRACTIONr_chiral_restr0.080.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028750
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021686
X-RAY DIFFRACTIONr_mcbond_it2.0053.2244352
X-RAY DIFFRACTIONr_mcbond_other2.0323.1784229
X-RAY DIFFRACTIONr_mcangle_it3.2844.6374849
LS refinement shellResolution: 1.909→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 246 -
Rwork0.355 4865 -
all-5111 -
obs--97.71 %
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)
11.88950.0221-1.06520.00790.02290.80380.13780.0642-0.01040.002-0.0378-0.013-0.0875-0.1554-0.10010.0154-0.00130.00680.15310.02530.0615-28.5913.154-45.517
20.70890.2335-0.24620.2634-0.45940.8797-0.02730.146-0.20480.0621-0.015-0.0685-0.12360.05710.04230.0431-0.0168-0.00290.0727-0.0280.0869-46.169-14.589-13.012
30.61480.1967-0.16490.17850.29611.1790.0762-0.0326-0.1067-0.0123-0.036-0.0605-0.0774-0.0251-0.04020.07030.010.00810.0670.00780.0284-2.611.389-51.049
40.38960.1313-0.08420.3681-0.44160.57610.0250.092-0.04410.0749-0.00090.0331-0.05710.0309-0.02410.08850.00090.01620.0341-0.00480.04719.265-13.591-5.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 298
2X-RAY DIFFRACTION2B106 - 298
3X-RAY DIFFRACTION2B301
4X-RAY DIFFRACTION3C106 - 298
5X-RAY DIFFRACTION3C301
6X-RAY DIFFRACTION4D108 - 298

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