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- PDB-1acf: ACANTHAMOEBA CASTELLANII PROFILIN IB -

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Basic information

Entry
Database: PDB / ID: 1acf
TitleACANTHAMOEBA CASTELLANII PROFILIN IB
ComponentsPROFILIN I
KeywordsCONTRACTILE PROTEIN / PROTEIN BINDING / PROFILIN / ACTIN-BINDING PROTEIN
Function / homology
Function and homology information


actin monomer binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / cytoskeleton / cytoplasm
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
Profilin-1A / Profilin-1B
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C.
CitationJournal: 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.
History
DepositionJul 29, 1994Processing site: BNL
Revision 1.0Aug 31, 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 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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 I


Theoretical massNumber of molelcules
Total (without water)12,8491
Polymers12,8491
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.031, 31.631, 33.487
Angle α, β, γ (deg.)90.00, 111.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROFILIN I /


Mass: 12849.333 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / References: UniProt: P68696, UniProt: Q95VF7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE USED IN THIS ENTRY WAS DERIVED FROM THAT OF POLLARD AND RIMM, CELL MOTILITY AND THE ...THE SEQUENCE USED IN THIS ENTRY WAS DERIVED FROM THAT OF POLLARD AND RIMM, CELL MOTILITY AND THE CYTOSKELETON, VOL. 20, 169-177, 1991. SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PRO1_ACACA SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE THR 1 SER 1 SER 4 THR 4 SER 31 THR 31 PHE 32 SER 32 SER 58 GLY 58 ALA 83 SER 83 ALA 84 SER 84

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
240 mM1dropKCl
35-10 mg/mlprotein1drop
41.1-1.8 M1reservoirLi2SO4
5100 mMHEPES1reservoir

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Data collection

ReflectionNum. obs: 5974 / % possible obs: 80.2 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 23.4 Å

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.179 -
obs0.179 5908
Displacement parametersBiso mean: 13.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 0 64 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_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_it2.192
X-RAY DIFFRACTIONx_mcangle_it3.0562
X-RAY DIFFRACTIONx_scbond_it3.3893
X-RAY DIFFRACTIONx_scangle_it4.4583
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_planar_d0.050.052

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