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- PDB-2acg: ACANTHAMOEBA CASTELLANII PROFILIN II -

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Basic information

Entry
Database: PDB / ID: 2acg
TitleACANTHAMOEBA CASTELLANII PROFILIN II
ComponentsPROFILIN II
KeywordsCONTRACTILE PROTEIN / PROTEIN BINDING / PROFILIN / ACTIN-BINDING PROTEIN
Function / homology
Function and homology information


actin monomer binding / cell cortex / cytoskeleton
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsFedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates.
Authors: Fedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C.
#1: Journal: Cell Motil.Cytoskeleton / Year: 1991
Title: Analysis of Cdna Clones for Acanthamoeba Profilin-I and Profilin-II Shows End to End Homology with Vertebrate Profilins and a Small Family of Profilin Genes
Authors: Pollard, T.D. / Rimm, D.L.
#2: Journal: Eur.J.Biochem. / Year: 1988
Title: The Primary Structure of the Basic Isoform of Acanthamoeba Profilin
Authors: Ampe, C. / Sato, M. / Pollard, T.D. / Vanderkerckhove, J.
History
DepositionAug 30, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SEVEN-STRANDED SHEET S1 DESCRIBED BELOW IS A SEVEN-STRANDED INCOMPLETE ANTIPARALLEL UP- ...SHEET THE SEVEN-STRANDED SHEET S1 DESCRIBED BELOW IS A SEVEN-STRANDED INCOMPLETE ANTIPARALLEL UP-AND-DOWN BETA BARREL. TWO STRANDS HAVE BETA-BULGES: LEU 70, ARG 71 AND TRP 29, ALA 30.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN II


Theoretical massNumber of molelcules
Total (without water)12,9371
Polymers12,9371
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.535, 47.951, 34.753
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROFILIN II


Mass: 12937.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Gene: CDNA / References: UniProt: P19984
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE WAS DERIVED FROM THAT OF POLLARD AND RIMM, CELL MOTILITY AND THE CYTOSKELETON, VOL. ...THE SEQUENCE WAS DERIVED FROM THAT OF POLLARD AND RIMM, CELL MOTILITY AND THE CYTOSKELETON, VOL. 20, 169-177, 1991.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
240 mM1dropKCl
35-10 mg/mlprotein1drop
42.0 Mammonium sulfate1reservoir
5100 mMHEPES1reservoir
62 %PEG4001reservoir

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Data collection

ReflectionNum. obs: 4479 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 4027
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 0 46 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg
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_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.8931.5
X-RAY DIFFRACTIONx_mcangle_it1.5232
X-RAY DIFFRACTIONx_scbond_it1.5262
X-RAY DIFFRACTIONx_scangle_it2.3873
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_planar_d0.050.04

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