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- PDB-6i13: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 7 -

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Basic information

Entry
Database: PDB / ID: 6i13
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 7
ComponentsFascin
KeywordsSTRUCTURAL PROTEIN / actin bundling / small molecule inhibition
Function / homology
Function and homology information


microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly / podosome / establishment or maintenance of cell polarity / microvillus / actin filament bundle assembly / stress fiber / positive regulation of lamellipodium assembly / ruffle / filopodium / regulation of actin cytoskeleton organization / cell motility / actin filament binding / cell migration / actin cytoskeleton / cell-cell junction / lamellipodium / actin binding / growth cone / cell cortex / actin cytoskeleton organization / protein-macromolecule adaptor activity / Interleukin-4 and Interleukin-13 signaling / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-H0Q / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSchuettelkopf, A.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.
Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / ...Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / McDonald, L. / Mezna, M. / Pannifer, A. / Paul, N.R. / Machesky, L. / McKinnon, H. / Bower, J.
History
DepositionOct 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2406
Polymers54,6021
Non-polymers6385
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint8 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.520, 92.240, 99.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fascin / 55 kDa actin-bundling protein / Singed-like protein / p55


Mass: 54601.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Plasmid: pBDDP-SPR3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q16658
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-H0Q / 2-[(3-chlorophenyl)methyl]-~{N}-(1-methylpyrazol-4-yl)-1-oxidanylidene-isoquinoline-4-carboxamide


Mass: 392.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.46 % / Mosaicity: 0.226 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18-22% PEG 8000, 100-130 mM MgAc2, 100 mM citric acid pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.79→60.52 Å / Num. obs: 53049 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.977 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Net I/σ(I): 11.8 / Num. measured all: 342076
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.504 / Mean I/σ(I) obs: 1.3 / Rpim(I) all: 0.68 / Rrim(I) all: 1.76 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia20.3.8.0data scaling
PDB_EXTRACT3.22data extraction
xia20.3.8.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I10

6i10


Resolution: 1.79→51.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.489 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.118
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2639 5 %RANDOM
Rwork0.1968 ---
obs0.1983 50343 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.41 Å2 / Biso mean: 34.38 Å2 / Biso min: 18.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 1.79→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 44 267 4095
Biso mean--34.46 39.16 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173397
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.675291
X-RAY DIFFRACTIONr_angle_other_deg1.6051.6597965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9385485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61521.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92215639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111533
X-RAY DIFFRACTIONr_chiral_restr0.1020.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024508
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02769
X-RAY DIFFRACTIONr_mcbond_it1.1891.7021941
X-RAY DIFFRACTIONr_mcbond_other1.1871.7021939
X-RAY DIFFRACTIONr_mcangle_it1.9382.5472425
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 196 -
Rwork0.346 3692 -
all-3888 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 16.48 Å / Origin y: 11.476 Å / Origin z: 26.448 Å
111213212223313233
T0.1812 Å2-0.0175 Å20.0181 Å2-0.1487 Å2-0.0121 Å2--0.004 Å2
L0.9939 °2-0.1296 °20.6704 °2-0.4464 °20.0941 °2--1.357 °2
S0.0445 Å °0.0719 Å °-0.0359 Å °-0.1123 Å °-0.0049 Å °-0.007 Å °-0.0083 Å °0.0451 Å °-0.0396 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 493
2X-RAY DIFFRACTION1A505
3X-RAY DIFFRACTION1A601 - 867
4X-RAY DIFFRACTION1A501 - 504

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