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- PDB-3fer: Crystal structure of n-terminal actin-binding domain from human f... -

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Basic information

Entry
Database: PDB / ID: 3fer
TitleCrystal structure of n-terminal actin-binding domain from human filamin b (tandem ch-domains). northeast structural genomics consortium target hr5571a.
ComponentsFilamin-B
Keywordsactin binding protein / X-RAY NESG HR5571A ACTIN-BINDING DOMAIN / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / ACTIN-BINDING / ALTERNATIVE SPLICING / CYTOPLASM / CYTOSKELETON / DEVELOPMENTAL PROTEIN / DIFFERENTIATION / DISEASE MUTATION / DWARFISM / MYOGENESIS / PHOSPHOPROTEIN / POLYMORPHISM
Function / homology
Function and homology information


epithelial cell morphogenesis / keratinocyte development / brush border / phagocytic vesicle / skeletal muscle tissue development / stress fiber / ISG15 antiviral mechanism / Z disc / cellular response to type II interferon / actin filament binding ...epithelial cell morphogenesis / keratinocyte development / brush border / phagocytic vesicle / skeletal muscle tissue development / stress fiber / ISG15 antiviral mechanism / Z disc / cellular response to type II interferon / actin filament binding / actin cytoskeleton / actin binding / cell cortex / actin cytoskeleton organization / cadherin binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Calponin-like domain / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Actin-binding Protein, T-fimbrin; domain 1 / Filamin/ABP280 repeat-like / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Calponin-like domain / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Actin-binding Protein, T-fimbrin; domain 1 / 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
ACETIC ACID / Filamin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, R. / Shastry, R. / Sahdev, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Huang, Y. / Acton, T. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, R. / Shastry, R. / Sahdev, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Huang, Y. / Acton, T. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of n-terminal actin-binding domain from human filamin b (tandem ch-domains). northeast structural genomics consortium target hr5571a.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, R. / Shastry, R. / Sahdev, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Huang, Y. / Acton, T. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Filamin-B
B: Filamin-B
C: Filamin-B
D: Filamin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2806
Polymers122,1604
Non-polymers1202
Water2,756153
1
A: Filamin-B


Theoretical massNumber of molelcules
Total (without water)30,5401
Polymers30,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Filamin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6002
Polymers30,5401
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Filamin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6002
Polymers30,5401
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Filamin-B


Theoretical massNumber of molelcules
Total (without water)30,5401
Polymers30,5401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.847, 82.410, 132.251
Angle α, β, γ (deg.)90.00, 94.14, 90.00
Int Tables number5
Space group name H-MC121
Detailsmonomer

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Components

#1: Protein
Filamin-B / FLN-B / Beta-filamin / Actin-binding-like protein / Thyroid autoantigen / Truncated actin-binding ...FLN-B / Beta-filamin / Actin-binding-like protein / Thyroid autoantigen / Truncated actin-binding protein / Truncated ABP / ABP-280 homolog / ABP-278 / Filamin 3 / Filamin homolog 1 / Fh1


Mass: 30539.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNB, FLN1L, FLN3, TABP, TAP / Production host: Escherichia coli (E. coli) / References: UniProt: O75369
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M SODIUM ACETATE, 18% PEG 3350, 0.1M SODIUM CHLORIDE, PH 4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 86206 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.8 / % possible all: 80.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKU

1wku


Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 107293.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3374 4.9 %RANDOM
Rwork0.215 ---
obs0.215 69145 72 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.6487 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å27.29 Å2
2---9.9 Å20 Å2
3---10.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7531 0 0 161 7692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 368 4.8 %
Rwork0.276 7220 -
obs--47.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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