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- PDB-4d60: Structure of a dimeric Plasmodium falciparum profilin mutant -

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Basic information

Entry
Database: PDB / ID: 4d60
TitleStructure of a dimeric Plasmodium falciparum profilin mutant
ComponentsPROFILIN
KeywordsSTRUCTURAL PROTEIN / ACTIN BINDING / DOMAIN SWAPPING
Function / homology
Function and homology information


cytoplasmic actin-based contraction involved in cell motility / sequestering of actin monomers / actin monomer binding / phospholipid binding / actin cytoskeleton / actin binding / cell cortex / actin cytoskeleton organization / cytoplasm
Similarity search - Function
Profilin, apicomplexa / : / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBhargav, S.P. / Vahokoski, J. / Kallio, J.P. / Torda, A. / Kursula, P. / Kursula, I.
CitationJournal: Cell.Mol.Life Sci. / Year: 2015
Title: Two Independently Folding Units of Plasmodium Profilin Suggest Evolution Via Gene Fusion.
Authors: Bhargav, S.P. / Vahokoski, J. / Kallio, J.P. / Torda, A.E. / Kursula, P. / Kursula, I.
History
DepositionNov 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Data collection / Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROFILIN
B: PROFILIN
C: PROFILIN
D: PROFILIN
E: PROFILIN
F: PROFILIN
G: PROFILIN
H: PROFILIN
I: PROFILIN
J: PROFILIN
K: PROFILIN
L: PROFILIN
M: PROFILIN
N: PROFILIN
O: PROFILIN
P: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,85924
Polymers300,09116
Non-polymers7698
Water0
1
E: PROFILIN
K: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6073
Polymers37,5112
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-28.4 kcal/mol
Surface area17160 Å2
MethodPISA
2
C: PROFILIN
D: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6073
Polymers37,5112
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-54.1 kcal/mol
Surface area17260 Å2
MethodPISA
3
J: PROFILIN
L: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6073
Polymers37,5112
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-37.1 kcal/mol
Surface area17200 Å2
MethodPISA
4
O: PROFILIN
P: PROFILIN


Theoretical massNumber of molelcules
Total (without water)37,5112
Polymers37,5112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-29.1 kcal/mol
Surface area17940 Å2
MethodPISA
5
B: PROFILIN
N: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8005
Polymers37,5112
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-56.4 kcal/mol
Surface area17740 Å2
MethodPISA
6
F: PROFILIN
H: PROFILIN


Theoretical massNumber of molelcules
Total (without water)37,5112
Polymers37,5112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-30.6 kcal/mol
Surface area17260 Å2
MethodPISA
7
G: PROFILIN
M: PROFILIN


Theoretical massNumber of molelcules
Total (without water)37,5112
Polymers37,5112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-29.8 kcal/mol
Surface area17300 Å2
MethodPISA
8
A: PROFILIN
I: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7034
Polymers37,5112
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-38.9 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.070, 246.460, 256.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PROFILIN /


Mass: 18755.686 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P86294, UniProt: Q8I2J4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 4.43 Å3/Da / Density % sol: 72.25 % / Description: NONE
Crystal growpH: 6
Details: 1.8 M AMMONIUM SULFATE, 0.1 M 2-(N- MORPHOLINO)ETHANESULFONIC ACID (PH 6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 154448 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 107.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.7 / % possible all: 98.3

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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 ENTRY 2JKF

2jkf


Resolution: 3.3→19.991 Å / SU ML: 0.48 / σ(F): 1.99 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 3985 4.9 %
Rwork0.2399 --
obs0.241 80619 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20227 0 40 0 20267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620659
X-RAY DIFFRACTIONf_angle_d1.12927999
X-RAY DIFFRACTIONf_dihedral_angle_d11.6397369
X-RAY DIFFRACTIONf_chiral_restr0.0453023
X-RAY DIFFRACTIONf_plane_restr0.0063661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.34010.44311390.39512722X-RAY DIFFRACTION100
3.3401-3.38210.40291280.37852728X-RAY DIFFRACTION100
3.3821-3.42640.42281460.37142666X-RAY DIFFRACTION99
3.4264-3.47310.37861280.34872731X-RAY DIFFRACTION100
3.4731-3.52250.39251360.33812715X-RAY DIFFRACTION100
3.5225-3.57480.32611330.31512692X-RAY DIFFRACTION100
3.5748-3.63030.36191300.30332712X-RAY DIFFRACTION99
3.6303-3.68950.27511200.28292724X-RAY DIFFRACTION100
3.6895-3.75270.34341390.27832703X-RAY DIFFRACTION100
3.7527-3.82040.35471400.27612750X-RAY DIFFRACTION100
3.8204-3.89340.311600.27982666X-RAY DIFFRACTION100
3.8934-3.97230.29591330.28052737X-RAY DIFFRACTION100
3.9723-4.05790.2861510.26872699X-RAY DIFFRACTION100
4.0579-4.15150.28661550.25362718X-RAY DIFFRACTION100
4.1515-4.25440.25111370.23622726X-RAY DIFFRACTION100
4.2544-4.36820.29521410.22362722X-RAY DIFFRACTION100
4.3682-4.49540.25161680.23222718X-RAY DIFFRACTION100
4.4954-4.63870.25281640.21372711X-RAY DIFFRACTION100
4.6387-4.80230.2221310.20212730X-RAY DIFFRACTION100
4.8023-4.99170.22911470.20972738X-RAY DIFFRACTION100
4.9917-5.21510.28771380.23522764X-RAY DIFFRACTION100
5.2151-5.48460.26391600.242721X-RAY DIFFRACTION100
5.4846-5.82030.23731540.24112733X-RAY DIFFRACTION99
5.8203-6.25690.24991360.24372796X-RAY DIFFRACTION100
6.2569-6.86330.25071430.2422771X-RAY DIFFRACTION100
6.8633-7.80420.25941570.22252797X-RAY DIFFRACTION100
7.8042-9.64510.17761310.17662847X-RAY DIFFRACTION99
9.6451-19.99140.19681400.19572897X-RAY DIFFRACTION98

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