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- PDB-2xf1: Crystal structure of Plasmodium falciparum actin depolymerization... -

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Basic information

Entry
Database: PDB / ID: 2xf1
TitleCrystal structure of Plasmodium falciparum actin depolymerization factor 1
ComponentsCOFILIN ACTIN-DEPOLYMERIZING FACTOR HOMOLOG 1
KeywordsACTIN-BINDING PROTEIN / CYTOSKELETON
Function / homology
Function and homology information


cytoplasmic actin-based contraction involved in cell motility / actin filament severing / actin filament depolymerization / actin monomer binding / actin filament binding / actin cytoskeleton / actin cytoskeleton organization / cytosol / 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 / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cofilin/actin-depolymerizing factor homolog 1
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSingh, B.K. / Sattler, J.M. / Huttu, J. / Chatterjee, M. / Schueler, H. / Kursula, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures Explain Functional Differences in the Two Actin Depolymerization Factors of the Malaria Parasite.
Authors: Singh, B.K. / Sattler, J.M. / Chatterjee, M. / Huttu, J. / Schuler, H. / Kursula, I.
History
DepositionMay 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Atomic model / Database references ...Atomic model / Database references / Other / Refinement description / Version format compliance
Revision 1.2Oct 19, 2011Group: Other
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COFILIN ACTIN-DEPOLYMERIZING FACTOR HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5695
Polymers14,1841
Non-polymers3844
Water3,369187
1
A: COFILIN ACTIN-DEPOLYMERIZING FACTOR HOMOLOG 1
hetero molecules

A: COFILIN ACTIN-DEPOLYMERIZING FACTOR HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,13710
Polymers28,3692
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2640 Å2
ΔGint-93.7 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.840, 68.840, 76.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

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Components

#1: Protein COFILIN ACTIN-DEPOLYMERIZING FACTOR HOMOLOG 1 / ACTIN DEPOLYMERIZATION FACTOR / ADF


Mass: 14184.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS24 AND CYS34 PARTIALLY OXIDIZED
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q8I467
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7.8 / Details: 2.5 M AMMONUIM SULFATE, 0.1 M HEPES PH 7.8, 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2010 / Details: MULTILAYER MIRROR
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14010 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 24.85 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 14.5 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1F7S, 1AHQ AND 2I2Q

1f7s

1ahq

2i2q


Resolution: 1.96→27.752 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 25.21 / Stereochemistry target values: ML
Details: INITIAL STAGES OF REFINEMENT WERE PERFORMED USING REFMAC 5
RfactorNum. reflection% reflection
Rfree0.2296 702 5 %
Rwork0.1872 --
obs0.1894 14010 90.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.275 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9512 Å20 Å20 Å2
2--0.9512 Å20 Å2
3----1.9024 Å2
Refinement stepCycle: LAST / Resolution: 1.96→27.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 20 187 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071053
X-RAY DIFFRACTIONf_angle_d1.0031437
X-RAY DIFFRACTIONf_dihedral_angle_d18.597395
X-RAY DIFFRACTIONf_chiral_restr0.081167
X-RAY DIFFRACTIONf_plane_restr0.003183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9582-2.10930.33961030.28481966X-RAY DIFFRACTION68
2.1093-2.32150.34581320.30062521X-RAY DIFFRACTION87
2.3215-2.65720.24481520.19352888X-RAY DIFFRACTION100
2.6572-3.34690.21551550.16782933X-RAY DIFFRACTION100
3.3469-27.75470.18021600.14853017X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89991.751.18692.30891.41781.02380.2209-0.0452-0.25450.0454-0.1563-0.2090.1038-0.1654-0.13230.2272-0.0137-0.06530.1683-0.02640.20821.0434.269111.2871
23.0396-3.8991-1.46635.02471.95750.9695-0.2515-0.1846-0.32490.2258-0.00460.7-0.0146-0.10960.27580.06680.03520.02630.1197-0.04860.158415.536318.647222.9165
30.6518-0.2467-0.33980.28430.27790.8473-0.086-0.1576-0.04680.01280.05650.05510.11020.10540.02730.19660.0397-0.00120.167-0.01810.118527.036516.657725.768
40.73570.1531-0.21610.26090.32280.8188-0.0143-0.00680.0938-0.1028-0.0337-0.0393-0.1783-0.06440.04040.16660.0094-0.00880.1115-0.00750.12230.242114.138316.7985
52.8759-0.07682.22140.3495-0.08072.0839-0.09350.15550.3812-0.2831-0.0649-0.0643-0.30110.15170.14440.2284-0.0018-0.02090.1119-0.00920.129829.592621.497314.3354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:7
2X-RAY DIFFRACTION2CHAIN A AND RESID 8:20
3X-RAY DIFFRACTION3CHAIN A AND RESID 21:57
4X-RAY DIFFRACTION4CHAIN A AND RESID 58:101
5X-RAY DIFFRACTION5CHAIN A AND RESID 102:114

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