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- PDB-6tj4: P. falciparum essential light chain, N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6tj4
TitleP. falciparum essential light chain, N-terminal domain
ComponentsPfELC
KeywordsMOTOR PROTEIN / motility / glideosome / myosin / essential light chain
Function / homologyEF-hand domain pair / Myosin essential light chain ELC
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPazicky, S. / Loew, C.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
Joachim Herz Foundation800026 Germany
Swedish Research Council621-2013-5905 Sweden
CitationJournal: Commun Biol / Year: 2020
Title: Structural role of essential light chains in the apicomplexan glideosome.
Authors: Pazicky, S. / Dhamotharan, K. / Kaszuba, K. / Mertens, H.D.T. / Gilberger, T. / Svergun, D. / Kosinski, J. / Weininger, U. / Low, C.
History
DepositionNov 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: PfELC
B: PfELC


Theoretical massNumber of molelcules
Total (without water)18,0422
Polymers18,0422
Non-polymers00
Water3,477193
1
A: PfELC


Theoretical massNumber of molelcules
Total (without water)9,0211
Polymers9,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PfELC


Theoretical massNumber of molelcules
Total (without water)9,0211
Polymers9,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.237, 57.510, 86.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein PfELC


Mass: 9021.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1017500 / Plasmid: pNIC28_Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IJM4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, lithium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→47.86 Å / Num. obs: 24622 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.12 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.02 / Rrim(I) all: 0.04 / Net I/σ(I): 17.68
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2365 / CC1/2: 0.89 / Rpim(I) all: 0.27 / Rrim(I) all: 0.57 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TJ3

6tj3


Resolution: 1.5→47.86 Å / SU ML: 0.1475 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9388
RfactorNum. reflection% reflection
Rfree0.1937 1174 4.77 %
Rwork0.1667 --
obs0.168 24621 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 193 1305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321159
X-RAY DIFFRACTIONf_angle_d1.16141559
X-RAY DIFFRACTIONf_chiral_restr0.0919154
X-RAY DIFFRACTIONf_plane_restr0.007201
X-RAY DIFFRACTIONf_dihedral_angle_d2.6207564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.30031580.27692818X-RAY DIFFRACTION98.28
1.57-1.650.27371320.23062906X-RAY DIFFRACTION99.05
1.65-1.750.21881330.19192897X-RAY DIFFRACTION99.05
1.75-1.890.21131560.17632912X-RAY DIFFRACTION99.26
1.89-2.080.20631500.16182900X-RAY DIFFRACTION99.32
2.08-2.380.16361360.15882943X-RAY DIFFRACTION99.13
2.38-30.20871460.17812985X-RAY DIFFRACTION98.96
Refinement TLS params.Method: refined / Origin x: 28.3640298791 Å / Origin y: 26.2041838222 Å / Origin z: 44.9284592006 Å
111213212223313233
T0.175787247752 Å2-0.00146080559286 Å20.0108301229517 Å2-0.444648760003 Å20.00717470210359 Å2--0.154179986743 Å2
L1.80537483671 °20.060864903693 °20.435603699614 °2-0.880771792697 °20.0829017750482 °2--2.16230278553 °2
S-0.0617382280218 Å °-0.0453515854874 Å °0.239909129988 Å °0.0339856600248 Å °0.0622616644807 Å °-0.0534219568712 Å °-0.221992373587 Å °0.0985138826159 Å °-0.0149952509949 Å °
Refinement TLS groupSelection details: all

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