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- PDB-1wlh: Molecular structure of the rod domain of Dictyostelium filamin -

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Basic information

Entry
Database: PDB / ID: 1wlh
TitleMolecular structure of the rod domain of Dictyostelium filamin
ComponentsGelation factor
KeywordsSTRUCTURAL PROTEIN / ABP-120 / filamin / Immunoglobulin fold / rod domain
Function / homology
Function and homology information


regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / phagocytosis / response to cAMP / extracellular matrix / cell motility / small GTPase binding / actin filament binding / cell migration / cell cortex / actin cytoskeleton organization / plasma membrane / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPopowicz, G.M. / Mueller, R. / Noegel, A.A. / Schleicher, M. / Huber, R. / Holak, T.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Molecular structure of the rod domain of dictyostelium filamin
Authors: Popowicz, G.M. / Mueller, R. / Noegel, A.A. / Schleicher, M. / Huber, R. / Holak, T.A.
History
DepositionJun 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Gelation factor
B: Gelation factor


Theoretical massNumber of molelcules
Total (without water)65,4502
Polymers65,4502
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-13 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.320, 61.670, 119.030
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gelation factor / Actin binding protein 120 / ABP-120 / ddFilamin


Mass: 32724.805 Da / Num. of mol.: 2 / Fragment: Repeat 4,5,6 ROD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: ABPC / Plasmid: PT7-7 , ECORI-SALI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P13466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: MPD, calcium chloride, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97891 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 68210 / Num. obs: 20708 / % possible obs: 99.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.026
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.124 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KSR

1ksr


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.06 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 1.109 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26315 1104 5.1 %RANDOM
Rwork0.25746 ---
obs0.25775 20708 99.04 %-
all-22012 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å2-3.25 Å2
2--1.34 Å20 Å2
3----5.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4537 0 0 88 4625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214703
X-RAY DIFFRACTIONr_bond_other_d00.024035
X-RAY DIFFRACTIONr_angle_refined_deg2.6771.9566398
X-RAY DIFFRACTIONr_angle_other_deg4.03839497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6125618
X-RAY DIFFRACTIONr_chiral_restr0.250.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.025442
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02872
X-RAY DIFFRACTIONr_nbd_refined0.2690.21139
X-RAY DIFFRACTIONr_nbd_other0.3050.24661
X-RAY DIFFRACTIONr_nbtor_other0.1310.22524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.590.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5680.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3430.25
X-RAY DIFFRACTIONr_mcbond_it0.6471.53063
X-RAY DIFFRACTIONr_mcangle_it1.12324935
X-RAY DIFFRACTIONr_scbond_it1.35331640
X-RAY DIFFRACTIONr_scangle_it2.2664.51463
LS refinement shellResolution: 2.8→2.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.402 81
Rwork0.396 1512

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