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- PDB-1nr0: Two Seven-Bladed Beta-Propeller Domains Revealed By The Structure... -

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Basic information

Entry
Database: PDB / ID: 1nr0
TitleTwo Seven-Bladed Beta-Propeller Domains Revealed By The Structure Of A C. elegans Homologue Of Yeast Actin Interacting Protein 1 (AIP1).
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 / regulation of locomotion / cortical actin cytoskeleton / 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 / regulation of locomotion / cortical actin cytoskeleton / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 / SIRAS / Resolution: 1.7 Å
AuthorsVorobiev, S.M. / Mohri, K. / 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.M. / Fedorov, A.A. / Almo, S.C. / Ono, S.
History
DepositionJan 23, 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: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4482
Polymers65,3931
Non-polymers551
Water12,773709
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.845, 65.174, 69.240
Angle α, β, γ (deg.)90.00, 98.28, 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, Mn chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 316K
Crystal grow
*PLUS
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: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 61821 / Num. obs: 61821 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.02 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.273 / Num. unique all: 6095 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 23.6 Å

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→23.59 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2503 4.1 %RANDOM
Rwork0.199 ---
all0.199 61801 --
obs0.199 61801 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.5878 Å2 / ksol: 0.366459 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å20 Å2-1.24 Å2
2--9.88 Å20 Å2
3----6.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 1 716 5298
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 415 4.2 %
Rwork0.288 9543 -
obs--95.7 %
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: 1.7 Å / Lowest resolution: 23.6 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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