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- PDB-1f2k: CRYSTAL STRUCTURE OF ACANTHAMOEBA CASTELLANII PROFILIN II, CUBIC ... -

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Basic information

Entry
Database: PDB / ID: 1f2k
TitleCRYSTAL STRUCTURE OF ACANTHAMOEBA CASTELLANII PROFILIN II, CUBIC CRYSTAL FORM
ComponentsPROFILIN II
KeywordsSTRUCTURAL PROTEIN / SEVEN-STRANDED INCOMPLETE ANTIPARALLEL UP-AND-DOWN BETA BARREL / ACTIN-BINDING PROTEIN / POLY-L-PROLINE BINDING PROTEIN / PIP2 BINDING PROTEIN
Function / homology
Function and homology information


actin binding / 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
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFedorov, A.A. / Shi, W. / Mahoney, N. / Kaiser, D.A. / Almo, S.C.
Citation
Journal: To be Published
Title: A Comparative Structural Analysis of Profilins
Authors: Fedorov, A.A. / Shi, W. / Mahoney, N. / Kaiser, D.A. / Almo, S.C.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Purification, Characterization and Crystallization of Human Platelet Profilin Expressed in Escherichia coli
Authors: Fedorov, A.A. / Pollard, T.D. / Almo, S.C.
#3: Journal: Structure / Year: 1997
Title: The Molecular Basis for Allergen Cross-Reactivity: Crystal Structure and IgE-Epitope Mapping of Birch Pollen Profilin
Authors: Fedorov, A.A. / Ball, T. / Mahoney, N. / Valenta, R. / Almo, S.C.
#4: Journal: J.STRUCT.BIOL. / Year: 1998
Title: Crystal Packing Induces a Conformational Change in Profilin-I from Acanthamoeba Castellanii
Authors: Liu, S. / Fedorov, A.A. / Pollard, T.D. / Lattman, E.E. / Almo, S.C. / Magnus, K.A.
#5: Journal: NAT.STRUCT.BIOL. / Year: 1999
Title: Profilin Binds Proline-Rich Ligands in Two Distinct Amido Backbone Orientations
Authors: Mahoney, N.M. / Rozwarski, D.A. / Fedorov, E.V. / Fedorov, A.A. / Almo, S.C.
History
DepositionMay 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PROFILIN II
B: PROFILIN II


Theoretical massNumber of molelcules
Total (without water)25,8752
Polymers25,8752
Non-polymers00
Water3,225179
1
A: PROFILIN II


Theoretical massNumber of molelcules
Total (without water)12,9371
Polymers12,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROFILIN II


Theoretical massNumber of molelcules
Total (without water)12,9371
Polymers12,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.524, 120.524, 120.524
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number212
Space group name H-MP4332
DetailsThe biological assembly is a monomer constructed from chain A or from chain B

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Components

#1: Protein PROFILIN II /


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.64 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: AMMONIUM SULFATE, SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 21, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 13681 / Num. obs: 13681 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 7.2 / % possible all: 99

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACG

2acg


Resolution: 2.3→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 622 5 %RANDOM
Rwork0.229 ---
all0.238 13681 --
obs0.232 12902 93.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 0 179 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.87
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it6.41.5
X-RAY DIFFRACTIONc_mcangle_it7.92
X-RAY DIFFRACTIONc_scbond_it8.92
X-RAY DIFFRACTIONc_scangle_it9.92.5
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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