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- PDB-1aoa: N-TERMINAL ACTIN-CROSSLINKING DOMAIN FROM HUMAN FIMBRIN -

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Basic information

Entry
Database: PDB / ID: 1aoa
TitleN-TERMINAL ACTIN-CROSSLINKING DOMAIN FROM HUMAN FIMBRIN
ComponentsT-FIMBRIN
KeywordsACTIN-BINDING PROTEIN / CALCIUM-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


actin filament network formation / actin filament bundle / actin filament bundle assembly / actin filament / bone development / actin filament binding / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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 ...Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsGoldsmith, S.C. / Pokala, N. / Shen, W. / Fedorov, A.A. / Matsudaira, P. / Almo, S.C.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The structure of an actin-crosslinking domain from human fimbrin.
Authors: Goldsmith, S.C. / Pokala, N. / Shen, W. / Fedorov, A.A. / Matsudaira, P. / Almo, S.C.
History
DepositionJun 30, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-FIMBRIN


Theoretical massNumber of molelcules
Total (without water)30,5321
Polymers30,5321
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.032, 61.241, 102.298
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 T-FIMBRIN


Mass: 30531.691 Da / Num. of mol.: 1 / Fragment: ABD1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P13797
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.88 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 8-20: PEG 8000, 20 MM CALCIUM ACETATE, 100MM SODIUM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMPIPES1drop
350 mM1dropNaCl
41 mM1dropMgCl2
50.1 mMEGTA1drop
61 mMdithiothreitol1drop
78-20 %PEG80001reservoir
820 mMcalcium acetate1reservoir
9100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. obs: 11764 / % possible obs: 80 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.217 / % possible all: 77.7
Reflection
*PLUS
Num. measured all: 39834
Reflection shell
*PLUS
% possible obs: 77.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.285 -10 %RANDOM
Rwork0.186 ---
obs0.186 10458 --
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 20 2333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.69
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.69
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.48

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