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- PDB-4akr: Crystal Structure of the cytoplasmic actin capping protein Cap32_... -

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Basic information

Entry
Database: PDB / ID: 4akr
TitleCrystal Structure of the cytoplasmic actin capping protein Cap32_34 from Dictyostelium discoideum
Components
  • F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA
  • F-ACTIN-CAPPING PROTEIN SUBUNIT BETA
KeywordsACTIN-BINDING PROTEIN
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / F-actin capping protein complex / barbed-end actin filament capping / response to bacterium / cell morphogenesis / actin filament binding / actin cytoskeleton organization / cytoplasm
Similarity search - Function
F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. ...F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Ribosomal protein S3 C-terminal domain / Aspartate Aminotransferase, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEckert, C. / Goretzki, A. / Faberova, M. / Kollmar, M.
CitationJournal: Bmc Struct.Biol. / Year: 2012
Title: Conservation and Divergence between Cytoplasmic and Muscle-Specific Actin Capping Proteins: Insights from the Crystal Structure of Cytoplasmic CAP32/34 from Dictyostelium Discoideum.
Authors: Eckert, C. / Goretzki, A. / Faberova, M. / Kollmar, M.
History
DepositionFeb 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA
B: F-ACTIN-CAPPING PROTEIN SUBUNIT BETA
C: F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA
D: F-ACTIN-CAPPING PROTEIN SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)128,1374
Polymers128,1374
Non-polymers00
Water5,945330
1
A: F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA
B: F-ACTIN-CAPPING PROTEIN SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)64,0692
Polymers64,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-40.5 kcal/mol
Surface area22990 Å2
MethodPISA
2
C: F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA
D: F-ACTIN-CAPPING PROTEIN SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)64,0692
Polymers64,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-43.1 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.460, 124.460, 77.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA / AGINACTIN SUBUNIT ALPHA / CAP34


Mass: 31194.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2
Description: CDNA FROM THE DICTYOSTELIUM CDNA PROJECT IN JAPAN AND THE JAPANESE NATIONAL BIORESOURCE PROJECT
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P13022
#2: Protein F-ACTIN-CAPPING PROTEIN SUBUNIT BETA / AGINACTIN SUBUNIT BETA / CAP32


Mass: 32873.859 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2
Description: CDNA FROM THE DICTYOSTELIUM CDNA PROJECT IN JAPAN AND THE JAPANESE NATIONAL BIORESOURCE PROJECT
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P13021
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES PH 7.5, 17% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60185 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.15
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.83 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IZN

1izn


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3010 5 %RANDOM
Rwork0.226 ---
obs0.226 60185 99.8 %-
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 0 330 8399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.359
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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