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- PDB-2wa5: Crystal structure of human filamin B actin binding domain at 1.9 ... -

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Basic information

Entry
Database: PDB / ID: 2wa5
TitleCrystal structure of human filamin B actin binding domain at 1.9 Angstroms resolution
ComponentsFILAMIN-B
KeywordsSTRUCTURAL PROTEIN / DISEASE MUTATION / SKELETAL DYSPLASIA / ACTIN-CROSSLINKING / MYOGENESIS / CYTOSKELETON / ACTIN-BINDING / CALPONIN HOMOLOGY DOMAIN / PHOSPHOPROTEIN / DIFFERENTIATION / ATELOSTEOGENESIS / MUTANT / FILAMIN / DWARFISM / CH DOMAIN / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


epithelial cell morphogenesis / keratinocyte development / brush border / skeletal muscle tissue development / stress fiber / phagocytic vesicle / cellular response to type II interferon / ISG15 antiviral mechanism / Z disc / actin filament binding ...epithelial cell morphogenesis / keratinocyte development / brush border / skeletal muscle tissue development / stress fiber / phagocytic vesicle / cellular response to type II interferon / ISG15 antiviral mechanism / Z disc / actin filament binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / cadherin binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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. ...Filamin family / Calponin-like domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Actin-binding Protein, T-fimbrin; domain 1 / 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 / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBONATE ION / Filamin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal ...Title: Disease-Associated Substitutions in the Filamin B Actin Binding Domain Confer Enhanced Actin Binding Affinity in the Absence of Major Structural Disturbance: Insights from the Crystal Structures of Filamin B Actin Binding Domains.
Authors: Sawyer, G.M. / Clark, A.R. / Robertson, S.P. / Sutherland-Smith, A.J.
History
DepositionFeb 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FILAMIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4716
Polymers28,1351
Non-polymers3365
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.050, 71.183, 90.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FILAMIN-B / BETA-FILAMIN / ACTIN-BINDING-LIKE PROTEIN / THYROID AUTOANTIGEN / TRUNCATED ACTIN-BINDING PROTEIN / ...BETA-FILAMIN / ACTIN-BINDING-LIKE PROTEIN / THYROID AUTOANTIGEN / TRUNCATED ACTIN-BINDING PROTEIN / ABP-280 HOMOLOG / ABP-278 / FILAMIN 3 / FILAMIN HOMOLOG 1 / FLN-B / TRUNCATED ABP / FH1 / W148R MUTANT FILAMIN B ACTIN-BINDING DOMAIN


Mass: 28135.186 Da / Num. of mol.: 1 / Fragment: ACTIN-BINDING DOMAIN, RESIDUES 2-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTB-FLNB-ABDWT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75369
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLEAVAGE WITH RTEV PROTEASE LEAVES THE LEADER GLY ALA MET ALA STARTING AT -2. CLONING INTO NCOI ...CLEAVAGE WITH RTEV PROTEASE LEAVES THE LEADER GLY ALA MET ALA STARTING AT -2. CLONING INTO NCOI CREATED MET ALA INSTEAD OF MET AT POSITION 1.

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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: 2.5 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5.7
Details: PROTEIN WAS CRYSTALLIZED FROM 1 M LITHIUM SULFATE, 0.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 5.7 AND 1 MM DTT

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 29, 2006 / Details: OSMIC BLUE CONFOCAL MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20.29 Å / Num. obs: 22614 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WKU

1wku


Resolution: 1.9→20.29 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.332 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES -2-1, 132-137 ARE DISORDERED. RESIDUES GLY ALA (-2 -1) AND GLY ASP ASP ASP ALA LYS (132- 137) WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1148 5.1 %RANDOM
Rwork0.191 ---
obs0.192 21416 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---0.76 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 21 281 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222036
X-RAY DIFFRACTIONr_bond_other_d0.0010.021392
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9652772
X-RAY DIFFRACTIONr_angle_other_deg0.95433423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4275249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45625.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5411511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_nbd_refined0.2020.2437
X-RAY DIFFRACTIONr_nbd_other0.1780.21444
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2971
X-RAY DIFFRACTIONr_nbtor_other0.0810.2920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.48431605
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69841977
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0843964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5974788
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 93
Rwork0.3 1541
Refinement TLS params.Method: refined / Origin x: -17.54 Å / Origin y: -10.072 Å / Origin z: 15.585 Å
111213212223313233
T-0.2318 Å20.0124 Å2-0.0094 Å2--0.1193 Å20.0047 Å2---0.1172 Å2
L1.0133 °20.3331 °2-0.3864 °2-0.4826 °2-0.0896 °2--0.9629 °2
S0.0063 Å °-0.07 Å °-0.0861 Å °0.0342 Å °-0.0455 Å °-0.0497 Å °0.0171 Å °-0.0087 Å °0.0391 Å °

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