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

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Basic information

Entry
Database: PDB / ID: 7fsg
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z56772132
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 / 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 / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / actin cytoskeleton organization / positive regulation of cell growth / blood microparticle / nuclear membrane / 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 / endoplasmic reticulum membrane / Neutrophil degranulation / 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
ALANINE / D-GLUTAMIC ACID / GLYCINE / Chem-YG9 / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.02 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)87,68824
Polymers85,7244
Non-polymers1,96520
Water6,485360
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)21,7985
Polymers21,4311
Non-polymers3674
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)22,70512
Polymers21,4311
Non-polymers1,27411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.040, 49.508, 115.578
Angle α, β, γ (deg.)90.000, 94.740, 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, 380 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-YG9 / (5R)-5-[2-(4-methoxyphenyl)ethyl]-5-methylimidazolidine-2,4-dione


Mass: 248.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 360 / 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: 2.7 Å3/Da / Density % sol: 54.37 % / 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: 2.02→115.22 Å / Num. obs: 60354 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.97 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.075 / Rrim(I) all: 0.142 / Net I/σ(I): 11.4 / Num. measured all: 208638 / 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
2.02-2.083.61.2491629345710.3320.7751.4730.998.4
8.81-115.223.10.05324798090.9460.0360.06461.899.9

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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: 2.02→115.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.78 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 2936 4.9 %RANDOM
Rwork0.2005 ---
obs0.203 57348 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110 Å2 / Biso mean: 42.955 Å2 / Biso min: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0 Å20.63 Å2
2---0.97 Å20 Å2
3---1.54 Å2
Refinement stepCycle: final / Resolution: 2.02→115.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 129 361 6398
Biso mean--52.69 45.81 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0148895
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157691
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.65310583
X-RAY DIFFRACTIONr_angle_other_deg1.2961.60417811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80123.207343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2631538
X-RAY DIFFRACTIONr_chiral_restr0.0780.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029252
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021761
X-RAY DIFFRACTIONr_mcbond_it1.8793.4274502
X-RAY DIFFRACTIONr_mcbond_other1.883.4234495
X-RAY DIFFRACTIONr_mcangle_it3.1174.9665061
LS refinement shellResolution: 2.021→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 198 -
Rwork0.361 4151 -
all-4349 -
obs--97.95 %
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)
11.4902-0.1621-0.67240.05260.16190.53890.0389-0.0068-0.1708-0.0373-0.06340.0126-0.1091-0.13290.02450.03650.04220.0190.1497-0.0050.1501-29.4163.241-45.657
20.6740.1716-0.14920.2713-0.50881.1408-0.03680.1814-0.23290.0957-0.0122-0.1179-0.190.01690.0490.0508-0.0383-0.03160.0821-0.0060.2005-46.5-14.72-13.028
30.75090.1846-0.28090.22140.33361.030.0478-0.0929-0.0887-0.0293-0.0336-0.0517-0.10820.0072-0.01420.0142-0.00460.00810.0718-0.00360.163-3.4432.102-51.43
40.58230.2183-0.07370.1989-0.18670.25670.04950.1033-0.02090.0741-0.00960.0452-0.04750.0608-0.03990.07620.00460.03470.0542-0.00860.14089.021-13.97-5.389
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 DIFFRACTION4D501 - 502

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