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- PDB-9fp8: Crystal structure of Anopheles gambiae actin depolymerizing factor -

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Basic information

Entry
Database: PDB / ID: 9fp8
TitleCrystal structure of Anopheles gambiae actin depolymerizing factor
ComponentsAGAP012056-PA
KeywordsSTRUCTURAL PROTEIN / actin binding protein / depolymerizing/severing protein
Function / homology
Function and homology information


regulation of cellular component biogenesis / regulation of cellular component organization / actin filament fragmentation / actin filament severing / actin filament binding / actin cytoskeleton / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLasiwa, D. / Kursula, I.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Febs J. / Year: 2025
Title: Crystal structure of Anopheles gambiae actin depolymerizing factor explains high affinity to monomeric actin.
Authors: Lasiwa, D. / Kursula, I.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGAP012056-PA
B: AGAP012056-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6557
Polymers34,1832
Non-polymers4725
Water1,78399
1
A: AGAP012056-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4685
Polymers17,0911
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGAP012056-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1872
Polymers17,0911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.014, 62.423, 87.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 34 or resid 36 through 143))
d_2ens_1(chain "B" and (resid 4 through 34 or resid 36 through 143))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYGLUGLUAA4 - 344 - 34
d_12GLNGLNARGARGAA36 - 14336 - 143
d_21GLYGLYGLUGLUBB4 - 344 - 34
d_22GLNGLNARGARGBB36 - 14336 - 143

NCS oper: (Code: givenMatrix: (0.999907507826, -0.00925020353658, 0.00997043269804), (-0.00926630150157, -0.999955835055, 0.00156958477408), (0.0099554733758, -0.00166182863526, -0.99994906214)Vector: ...NCS oper: (Code: given
Matrix: (0.999907507826, -0.00925020353658, 0.00997043269804), (-0.00926630150157, -0.999955835055, 0.00156958477408), (0.0099554733758, -0.00166182863526, -0.99994906214)
Vector: 28.2921475828, 5.3726095261, -43.5875447821)

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Components

#1: Protein AGAP012056-PA


Mass: 17091.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1280611, AgaP_AGAP012056 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0NGL9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.17 M ammonium sulphate, 25.5% w/v polyethylene glycol 4000, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 1.68→47.14 Å / Num. obs: 444998 / % possible obs: 98.47 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.99 / Net I/σ(I): 3.77
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 3067 / CC1/2: 0.294

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→47.14 Å / SU ML: 0.3154 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 41.4865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3382 3325 5.01 %
Rwork0.2971 63029 -
obs0.2992 66354 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.99 Å2
Refinement stepCycle: LAST / Resolution: 1.68→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 27 99 2400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01842344
X-RAY DIFFRACTIONf_angle_d1.21353134
X-RAY DIFFRACTIONf_chiral_restr0.074329
X-RAY DIFFRACTIONf_plane_restr0.0119396
X-RAY DIFFRACTIONf_dihedral_angle_d14.146904
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.656943345185 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.4092800.49631558X-RAY DIFFRACTION58.02
1.7-1.730.43791410.42972667X-RAY DIFFRACTION99.89
1.73-1.750.49511450.42492695X-RAY DIFFRACTION100
1.75-1.780.41461370.39722698X-RAY DIFFRACTION99.89
1.78-1.810.3921390.38852652X-RAY DIFFRACTION100
1.81-1.850.40321370.37082680X-RAY DIFFRACTION99.65
1.85-1.880.46031420.37312685X-RAY DIFFRACTION99.72
1.88-1.920.35921420.34592651X-RAY DIFFRACTION99.68
1.92-1.960.36011420.33492648X-RAY DIFFRACTION99.36
1.96-2.010.36461420.30782693X-RAY DIFFRACTION99.44
2.01-2.060.30311390.30762661X-RAY DIFFRACTION99.36
2.06-2.110.38911410.29592651X-RAY DIFFRACTION99.39
2.11-2.170.37491390.29142690X-RAY DIFFRACTION99.86
2.17-2.250.29351480.30022692X-RAY DIFFRACTION99.93
2.25-2.330.32181430.2942672X-RAY DIFFRACTION99.4
2.33-2.420.36971420.29532657X-RAY DIFFRACTION99.68
2.42-2.530.33391380.28852691X-RAY DIFFRACTION99.96
2.53-2.660.28571420.29542666X-RAY DIFFRACTION99.82
2.66-2.830.35261430.2932659X-RAY DIFFRACTION99.82
2.83-3.050.32261410.28612685X-RAY DIFFRACTION99.51
3.05-3.350.3341410.28772659X-RAY DIFFRACTION99.15
3.35-3.840.33191390.25622673X-RAY DIFFRACTION99.68
3.84-4.830.25781400.23472681X-RAY DIFFRACTION99.65
4.84-47.140.32471420.26232665X-RAY DIFFRACTION99.36
Refinement TLS params.Method: refined / Origin x: 13.6699340344 Å / Origin y: 2.51535469725 Å / Origin z: -21.9693085407 Å
111213212223313233
T0.261967754435 Å2-0.0169790830909 Å2-0.212959622277 Å2-0.134343147748 Å2-0.00801596078905 Å2--0.356062036743 Å2
L0.242035246818 °20.0997925020133 °20.041754363243 °2-0.342444255101 °20.118646719036 °2--0.145097279704 °2
S0.0127272924272 Å °-0.0340210246341 Å °0.0066638994085 Å °0.0136456847896 Å °-0.0135540456955 Å °-0.166559130897 Å °-0.00961605142606 Å °0.0244085866974 Å °-0.0132691956191 Å °
Refinement TLS groupSelection details: all

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