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- PDB-6i15: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 11 -

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Basic information

Entry
Database: PDB / ID: 6i15
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 11
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 / podosome / positive regulation of podosome assembly / cell-cell junction 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 / podosome / positive regulation of podosome assembly / cell-cell junction assembly / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / microvillus / actin filament bundle assembly / positive regulation of lamellipodium assembly / stress fiber / ruffle / filopodium / cell motility / regulation of actin cytoskeleton organization / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / actin binding / cell cortex / growth cone / actin cytoskeleton organization / 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-GZT / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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)55,1075
Polymers54,6021
Non-polymers5054
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint7 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.180, 92.370, 97.390
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GZT / 1-[[2,2-bis(fluoranyl)-1,3-benzodioxol-5-yl]methyl]-~{N}-methyl-2-oxidanylidene-pyridine-3-carboxamide


Mass: 322.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12F2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.52 Å3/Da / Density % sol: 51.19 % / Mosaicity: 0.313 °
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→43.08 Å / Num. obs: 43448 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.427 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Net I/σ(I): 11.9
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.5 / Rpim(I) all: 0.603 / Rrim(I) all: 1.511 / % possible all: 99.8

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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: 1.91→43.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.217 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.147
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2136 4.9 %RANDOM
Rwork0.203 ---
obs0.205 41257 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91 Å2 / Biso mean: 42.721 Å2 / Biso min: 23.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--1.49 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.91→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 35 174 3993
Biso mean--40.18 43.67 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173396
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.6655295
X-RAY DIFFRACTIONr_angle_other_deg1.5891.6547966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8225487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62921.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18715642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7321533
X-RAY DIFFRACTIONr_chiral_restr0.1030.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024512
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02766
X-RAY DIFFRACTIONr_mcbond_it1.6712.6451946
X-RAY DIFFRACTIONr_mcbond_other1.6692.6441944
X-RAY DIFFRACTIONr_mcangle_it2.6153.9592433
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 149 -
Rwork0.353 2979 -
all-3128 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 16.097 Å / Origin y: 11.908 Å / Origin z: 25.136 Å
111213212223313233
T0.0205 Å2-0.0148 Å20.0278 Å2-0.1256 Å2-0.0376 Å2--0.0449 Å2
L1.4155 °2-0.0721 °20.8499 °2-0.5644 °2-0.2012 °2--1.917 °2
S0.0559 Å °0.1156 Å °0.0601 Å °-0.0199 Å °-0.0017 Å °0.0142 Å °0.0004 Å °0.0182 Å °-0.0542 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 493
2X-RAY DIFFRACTION1A504
3X-RAY DIFFRACTION1A601 - 774
4X-RAY DIFFRACTION1A501 - 503

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