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- PDB-4wsf: Falafel EVH1 domain bound to CENP-C FIM -

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Basic information

Entry
Database: PDB / ID: 4wsf
TitleFalafel EVH1 domain bound to CENP-C FIM
Components
  • Cenp-C
  • Serine/threonine-protein phosphatase 4 regulatory subunit 3
KeywordsSIGNALING PROTEIN / phosphatase EVH1 domain
Function / homology
Function and homology information


protein phosphatase 4 complex / basal protein localization / asymmetric neuroblast division / regulation of centromere complex assembly / female meiosis chromosome segregation / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / regulation of stem cell differentiation / protein localization to kinetochore ...protein phosphatase 4 complex / basal protein localization / asymmetric neuroblast division / regulation of centromere complex assembly / female meiosis chromosome segregation / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / regulation of stem cell differentiation / protein localization to kinetochore / mitotic metaphase chromosome alignment / chromosome, centromeric region / chromosome segregation / kinetochore / DNA repair / membrane / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein phosphatase 4 regulatory subunit 3-like, central domain / Phosphatase 4 regulatory subunit 3 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 4 regulatory subunit 3 / Centromeric protein-C, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsLefevre, S.R. / Singleton, M.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Centromeric binding and activity of Protein Phosphatase 4.
Authors: Lipinszki, Z. / Lefevre, S. / Savoian, M.S. / Singleton, M.R. / Glover, D.M. / Przewloka, M.R.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 4 regulatory subunit 3
B: Cenp-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1083
Polymers16,0122
Non-polymers961
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-18 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.755, 67.755, 53.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Serine/threonine-protein phosphatase 4 regulatory subunit 3 / PP4R3 / Protein falafel


Mass: 13984.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: flfl, CG9351 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VFS5
#2: Protein/peptide Cenp-C / FI18815p1


Mass: 2027.299 Da / Num. of mol.: 1 / Fragment: UNP residues 1048-1066 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VHP9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→58.68 Å / Num. obs: 22313 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Net I/σ(I): 11.7 / Num. measured all: 150514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.5-1.536.80.971.7724310580.6560.39496.5
8.22-58.686.70.04238.610131520.9990.01799.9

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Processing

Software
NameVersionClassification
XDS0.2.17data reduction
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
PHENIXrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XOD, 1RRP

1xod

1rrp


Resolution: 1.501→58.678 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1764 1162 5.21 %
Rwork0.1343 21144 -
obs0.1364 22306 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.25 Å2 / Biso mean: 34.1018 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 1.501→58.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 5 85 1061
Biso mean--44.56 41.64 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009991
X-RAY DIFFRACTIONf_angle_d1.1741340
X-RAY DIFFRACTIONf_chiral_restr0.045149
X-RAY DIFFRACTIONf_plane_restr0.005173
X-RAY DIFFRACTIONf_dihedral_angle_d12.834373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5007-1.5690.25871490.1962603275298
1.569-1.65180.23821470.176926202767100
1.6518-1.75530.22481290.158126522781100
1.7553-1.89080.22661550.133326302785100
1.8908-2.08110.16541450.115526182763100
2.0811-2.38220.151620.107926482810100
2.3822-3.00130.17131240.138526752799100
3.0013-58.72240.16461510.133626982849100

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