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- PDB-4b7l: Crystal Structure of Human Filamin B Actin Binding Domain with 1s... -

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Basic information

Entry
Database: PDB / ID: 4b7l
TitleCrystal Structure of Human Filamin B Actin Binding Domain with 1st Filamin Repeat
ComponentsFILAMIN-B
KeywordsSTRUCTURAL PROTEIN / FR 1 FILAMIN HINGE ABD-1
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSawyer, G.M. / Sutherland-Smith, A.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of the Filamin N-Terminal Region Reveals a Hinge between the Actin Binding and First Repeat Domains
Authors: Sawyer, G.M. / Sutherland-Smith, A.J.
History
DepositionAug 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Atomic model / Database references / Other
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FILAMIN-B
B: FILAMIN-B


Theoretical massNumber of molelcules
Total (without water)78,5722
Polymers78,5722
Non-polymers00
Water7,584421
1
A: FILAMIN-B


Theoretical massNumber of molelcules
Total (without water)39,2861
Polymers39,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FILAMIN-B


Theoretical massNumber of molelcules
Total (without water)39,2861
Polymers39,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.180, 69.690, 73.460
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39285.828 Da / Num. of mol.: 2
Fragment: ACTIN-BINDING DOMAIN WITH REPEAT 1, RESIDUES 1-347
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ABD-1 HINGE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75369
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.2 Å3/Da / Density % sol: 44.3 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG 4000, 0.1 M TRIS HCL PH 8.5, 0.2 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2011 / Details: 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: 2.05→35.7 Å / Num. obs: 41595 / % possible obs: 97.5 % / Observed criterion σ(I): 2.5 / Redundancy: 4.2 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WA5

2wa5


Resolution: 2.05→35.738 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 23.38 / Stereochemistry target values: ML
Details: RESIDUES 1-12 ARE DISORDERED. RESIDUES IN THE CH1-CH2 LINK ARE DISORDERED, IN CHAIN A 130-136 AND IN CHAIN B 132-136
RfactorNum. reflection% reflection
Rfree0.219 2094 5 %
Rwork0.1831 --
obs0.185 41576 97.09 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1.8 Å2 / ksol: 1.8 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 0 421 5686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025464
X-RAY DIFFRACTIONf_angle_d0.5987430
X-RAY DIFFRACTIONf_dihedral_angle_d12.1922102
X-RAY DIFFRACTIONf_chiral_restr0.037816
X-RAY DIFFRACTIONf_plane_restr0.002958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.09770.30071240.2672576X-RAY DIFFRACTION95
2.0977-2.15020.30561550.25182542X-RAY DIFFRACTION96
2.1502-2.20830.23441230.23452598X-RAY DIFFRACTION96
2.2083-2.27330.29391090.21732616X-RAY DIFFRACTION96
2.2733-2.34660.26881370.20972602X-RAY DIFFRACTION96
2.3466-2.43050.24061300.20232599X-RAY DIFFRACTION96
2.4305-2.52780.24061440.1982622X-RAY DIFFRACTION97
2.5278-2.64280.24071610.19932600X-RAY DIFFRACTION97
2.6428-2.7820.231490.19192627X-RAY DIFFRACTION97
2.782-2.95630.24291320.20022652X-RAY DIFFRACTION98
2.9563-3.18440.25721430.18952644X-RAY DIFFRACTION98
3.1844-3.50460.20811380.17062681X-RAY DIFFRACTION98
3.5046-4.01110.17961460.15662690X-RAY DIFFRACTION99
4.0111-5.05130.19131370.14922685X-RAY DIFFRACTION99
5.0513-35.74330.17891660.1672748X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1014-0.28230.68662.69931.33056.07370.09030.03530.0948-0.2221-0.06450.18870.1569-0.1767-0.01880.36870.0286-0.0060.210.03690.217517.4532-6.23515.7993
22.17390.6436-0.14922.10340.35845.2689-0.0072-0.0443-0.02370.38760.0469-0.02360.13060.0962-0.03530.4366-0.0038-0.01440.1949-0.01960.22224.01473.769539.6797
36.20090.4602-1.57725.10340.44395.57070.0121-0.14950.21990.10760.2589-0.1529-0.16140.2634-0.24890.2882-0.0143-0.01490.282-0.06650.26739.345212.515775.4593
41.6023-0.05870.60822.3729-0.86024.0973-0.00590.0830.08180.09150.04250.0292-0.10130.0592-0.03850.4836-0.0101-0.10470.2982-0.01690.2968-9.19823.712852.5165
51.5789-0.0669-0.75023.22050.32813.4463-0.08360.13010.018-0.133-0.0147-0.0575-0.1266-0.12040.1010.4075-0.0038-0.11830.30810.04280.3072-14.217412.451628.2164
66.61256.3372-1.27517.2807-2.71656.1518-0.18320.18520.0553-0.28510.2249-0.2294-0.08670.2343-0.07270.54040.03580.09240.51630.03410.67216.622324.39314.7149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 13:134 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 136:251 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 252:347 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 13:134 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 136:251 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 252:347 )

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