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- PDB-1pev: Crystal Structure of the Actin Interacting Protein from Caenorhab... -

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Basic information

Entry
Database: PDB / ID: 1pev
TitleCrystal Structure of the Actin Interacting Protein from Caenorhabditis Elegans
ComponentsActin interacting protein 1
KeywordsSTRUCTURAL PROTEIN / BETA PROPELLER / WD40 REPEAT / ACTIN INTERACTING PROTEIN / ADF / COFILIN / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / actin filament depolymerization / locomotion / sarcomere organization / cortical actin cytoskeleton / regulation of locomotion / myofibril / skeletal muscle thin filament assembly ...muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / actin filament depolymerization / locomotion / sarcomere organization / cortical actin cytoskeleton / regulation of locomotion / myofibril / skeletal muscle thin filament assembly / sarcoplasm / actin filament binding / actin binding
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Actin-interacting protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVorobiev, S. / Mohri, K. / Fedorov, A.A. / Ono, S. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments.
Authors: Mohri, K. / Vorobiev, S. / Fedorov, A.A. / Almo, S.C. / Ono, S.
History
DepositionMay 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Aug 16, 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

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Assembly

Deposited unit
A: Actin interacting protein 1


Theoretical massNumber of molelcules
Total (without water)65,3931
Polymers65,3931
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.660, 90.817, 76.983
Angle α, β, γ (deg.)90.00, 94.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Actin interacting protein 1 / AIP1 / Uncoordinated protein 78


Mass: 65392.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: UNC-78 OR C04F6.4 / Plasmid: PET-UNC-78 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q11176
#2: Water ChemComp-HOH / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 8000, MES, manganese chloride, glycerol, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13-4 mg/mlprotein1drop
20.1 MMES1reservoir
320 %PEG80001reservoir
410 mM1reservoirMnCl2
53 %glycerol1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 36740 / Num. obs: 36740 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.97 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.256 / Num. unique all: 3295 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 21.7 Å
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NR0

1nr0


Resolution: 2→21.72 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1471 4 %RANDOM
Rwork0.197 ---
obs0.197 36698 97.2 %-
all-36698 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3406 Å2 / ksol: 0.371561 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å23.56 Å2
2---3.75 Å20 Å2
3---0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→21.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 0 330 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scbond_it3.152
X-RAY DIFFRACTIONc_scangle_it4.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 235 4 %
Rwork0.251 5596 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PROTEIN_RETOPHCSDX.P
X-RAY DIFFRACTION3PARAM11.WATOPH19.SOL
X-RAY DIFFRACTION4PARAMETER.TOPOLOGY.EL
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 21.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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