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- PDB-3v8o: Human Filamin C Ig - like Domains 4 and 5 -

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Basic information

Entry
Database: PDB / ID: 3v8o
TitleHuman Filamin C Ig - like Domains 4 and 5
ComponentsFilamin-C
KeywordsSTRUCTURAL PROTEIN / Immunoglobulin like Fold / Muscle Z Disk
Function / homology
Function and homology information


Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding ...Cell-extracellular matrix interactions / costamere / ankyrin binding / sarcomere organization / sarcoplasm / intercellular bridge / cytoskeletal protein binding / sarcolemma / Z disc / actin filament binding / cytoskeleton / focal adhesion / identical protein binding / plasma membrane / cytosol / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSethi, R. / Ylanne, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A novel structural unit in the N-terminal region of filamins.
Authors: Sethi, R. / Seppala, J. / Tossavainen, H. / Ylilauri, M. / Ruskamo, S. / Pentikainen, O.T. / Pentikainen, U. / Permi, P. / Ylanne, J.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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-C
B: Filamin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2503
Polymers41,2102
Non-polymers391
Water84747
1
A: Filamin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6442
Polymers20,6051
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Filamin-C


Theoretical massNumber of molelcules
Total (without water)20,6051
Polymers20,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.620, 91.350, 103.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGSERSERAA575 - 6128 - 45
21ARGARGSERSERBB575 - 6128 - 45
12CYSCYSGLUGLUAA618 - 76051 - 193
22CYSCYSGLUGLUBB618 - 76051 - 193

NCS ensembles :
ID
1
2

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Components

#1: Protein Filamin-C / FLN-C / FLNc / ABP-280-like protein / ABP-L / Actin-binding-like protein / Filamin-2 / Gamma-filamin


Mass: 20605.201 Da / Num. of mol.: 2 / Fragment: Domains 4 and 5 (UNP residues 569-761)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABPL, FLN2, FLNC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q14315
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.67 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M Sodium Potassium Phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.8→46.633 Å / Num. obs: 15138 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 32.52 Å2
Reflection shellHighest resolution: 2.8 Å / % possible all: 98

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NQC

2nqc


Resolution: 2.8→46.63 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.288 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.701 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 1512 10 %RANDOM
Rwork0.20032 ---
all0.20565 15114 --
obs0.20565 13602 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: 29.295 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20 Å2
2---2.57 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 1 47 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222929
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9713989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4135378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75525120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.115447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7871512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222276
X-RAY DIFFRACTIONr_mcbond_it0.9411.51893
X-RAY DIFFRACTIONr_mcangle_it1.83923066
X-RAY DIFFRACTIONr_scbond_it2.58131036
X-RAY DIFFRACTIONr_scangle_it4.6954.5923
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11152tight positional0.050.05
22572tight positional0.090.05
11117medium positional0.060.5
22513medium positional0.150.5
11152tight thermal0.130.5
22572tight thermal0.130.5
11117medium thermal0.132
22513medium thermal0.152
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 113 -
Rwork0.334 1012 -
obs--100 %

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