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- PDB-7ft9: SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP... -

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Entry
Database: PDB / ID: 7ft9
TitleSDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z45636695
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
4-[(METHYLSULFONYL)AMINO]BENZOIC ACID / ALANINE / D-GLUTAMIC ACID / GLYCINE / Syntenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.77 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)87,19520
Polymers85,7244
Non-polymers1,47116
Water5,513306
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)21,8455
Polymers21,4311
Non-polymers4144
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)80.845, 49.152, 115.021
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, 322 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / 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-4MB / 4-[(METHYLSULFONYL)AMINO]BENZOIC ACID


Mass: 215.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO4S / 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.: 3 / 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.: 306 / 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: 2.66 Å3/Da / Density % sol: 53.68 % / 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: 1.77→80.53 Å / Num. obs: 87561 / % possible obs: 99.3 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 11.5 / Num. measured all: 597419 / 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
1.77-1.85.42.5922203440810.3521.2162.8770.391.8
9.53-80.536.60.04341456300.9930.020.04767.199.8

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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: 1.77→80.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.792 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 4245 4.9 %RANDOM
Rwork0.2055 ---
obs0.2075 82379 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 330.53 Å2 / Biso mean: 41.544 Å2 / Biso min: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1--15.48 Å2-0 Å27.59 Å2
2---4.59 Å20 Å2
3---20.07 Å2
Refinement stepCycle: final / Resolution: 1.77→80.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 93 306 6307
Biso mean--63.12 46 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0148143
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157092
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.6389886
X-RAY DIFFRACTIONr_angle_other_deg1.3381.59316390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86922.225373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.736151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9351553
X-RAY DIFFRACTIONr_chiral_restr0.10.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028678
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021700
X-RAY DIFFRACTIONr_mcbond_it2.6383.6254050
X-RAY DIFFRACTIONr_mcbond_other2.6613.5693961
X-RAY DIFFRACTIONr_mcangle_it3.85.3194672
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 246 -
Rwork0.418 4973 -
all-5219 -
obs--80.02 %
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)
10.6299-0.2533-0.17370.11590.11030.23790.01-0.0483-0.2323-0.0354-0.00870.0892-0.128-0.0062-0.00130.08250.02130.02890.0693-0.00540.1182-29.1272.953-45.1
20.51520.1138-0.05310.1748-0.26990.4629-0.01030.0908-0.09180.0477-0.012-0.0417-0.0770.03740.02220.0351-0.0057-0.01460.0319-0.00090.0642-46.314-14.459-12.864
30.29630.0012-0.06350.18640.30810.53010.0245-0.0407-0.0795-0.0520.0065-0.0336-0.08940.0076-0.03110.03410.0014-0.00340.0365-0.00650.0404-3.2041.936-50.985
40.23060.0824-0.07630.1687-0.23870.3840.03060.0595-0.03030.0531-0.01170.0253-0.03910.028-0.01890.0578-0.00740.01830.0246-0.01250.05079.308-13.776-5.207
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

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