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

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Basic information

Entry
Database: PDB / ID: 7ftc
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1509711879
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 / positive regulation of JNK cascade / adherens junction / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / blood microparticle / 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 / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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-YFR / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.87 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)87,76522
Polymers85,7244
Non-polymers2,04118
Water5,423301
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)21,9656
Polymers21,4311
Non-polymers5345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Syntenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,60510
Polymers21,4311
Non-polymers1,1749
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.205, 49.200, 114.858
Angle α, β, γ (deg.)90.000, 95.240, 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, 319 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-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-YFR / 6-bromo-7-hydroxy-2,2-dimethyl-2H,4H-1,3-benzodioxin-4-one


Mass: 273.080 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9BrO4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 301 / 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: 53.28 % / 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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.87→57.17 Å / Num. obs: 74374 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Net I/σ(I): 9.2 / Num. measured all: 513339 / 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
1.87-1.9172.93135344580.4081.1733.1310.297.2
9.15-57.176.60.04246587070.9870.0190.04759.499.6

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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: 1.87→57.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 17.686 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 3466 4.9 %RANDOM
Rwork0.2095 ---
obs0.2117 67715 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.14 Å2 / Biso mean: 50.743 Å2 / Biso min: 30.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.86 Å2
2--0.27 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.87→57.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 123 301 6332
Biso mean--72.15 54.12 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0148342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157264
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6610057
X-RAY DIFFRACTIONr_angle_other_deg1.2851.616819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8715974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07523.114334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.663151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0061538
X-RAY DIFFRACTIONr_chiral_restr0.0790.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028641
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021643
X-RAY DIFFRACTIONr_mcbond_it2.0743.654148
X-RAY DIFFRACTIONr_mcbond_other2.0943.5844059
X-RAY DIFFRACTIONr_mcangle_it3.3535.2844732
LS refinement shellResolution: 1.869→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 132 -
Rwork0.502 2540 -
all-2672 -
obs--48.88 %
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)
11.3848-0.1524-0.57770.04850.16850.60630.00240.0212-0.2224-0.0331-0.06390.0265-0.1229-0.16380.06150.04280.03430.02520.2320.00850.2528-28.7623.141-45.324
20.7850.2047-0.31590.413-0.82251.7867-0.08490.2408-0.25750.1491-0.0051-0.1508-0.3194-0.03750.08990.0867-0.0454-0.01330.1671-0.01370.3452-45.923-14.769-13.018
30.46090.2217-0.21220.32270.40261.30540.0396-0.0498-0.151-0.0267-0.0284-0.143-0.12110.0166-0.01120.01320.00040.00960.15410.00480.3153-2.8522.004-50.834
40.41430.00190.03390.2635-0.08610.04540.01340.1098-0.03020.0821-0.00790.0645-0.00870.0448-0.00540.0490.02610.04280.17450.00740.22479.239-13.834-5.231
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 DIFFRACTION3C301
5X-RAY DIFFRACTION4D108 - 298
6X-RAY DIFFRACTION4D301 - 302

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