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- PDB-1ahq: RECOMBINANT ACTOPHORIN -

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Basic information

Entry
Database: PDB / ID: 1ahq
TitleRECOMBINANT ACTOPHORIN
ComponentsACTOPHORIN
KeywordsACTIN BINDING PROTEIN / ACTOPHORIN
Function / homology
Function and homology information


actin filament depolymerization / actin cytoskeleton / actin binding / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / MIR X-RAY CRYSTAL / Resolution: 2.3 Å
AuthorsLeonard, S.A. / Gittis, A.G. / Petrella, E.C. / Pollard, T.D. / Lattman, E.E.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the actin-binding protein actophorin from Acanthamoeba.
Authors: Leonard, S.A. / Gittis, A.G. / Petrella, E.C. / Pollard, T.D. / Lattman, E.E.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Sep 4, 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTOPHORIN


Theoretical massNumber of molelcules
Total (without water)15,4441
Polymers15,4441
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.295, 47.486, 67.585
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 ACTOPHORIN


Mass: 15444.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Cell line: BL21 / Plasmid: PACT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37167
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5
Details: 20-25% PEG 8000, 100MM HEPES (PH7.5), 10% ISOPROPANOL, 1MM DTT
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
210 %isopropanol1reservoir
31 mMdithiothreitol1reservoir
420-25 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→10 Å / Num. obs: 7897 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.19 / Rsym value: 0.6
Reflection shellResolution: 2.06→2.25 Å / Mean I/σ(I) obs: 5.3 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 26016 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR X-RAY CRYSTAL / Resolution: 2.3→6 Å / σ(F): 6
RfactorNum. reflection% reflection
Rfree0.32 --
Rwork0.21 --
obs0.21 4809 85.9 %
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 71 1125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
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
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 -10 %
Rwork0.38 103 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor obs: 0.38

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