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- PDB-2jkf: Plasmodium falciparum profilin -

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Basic information

Entry
Database: PDB / ID: 2jkf
TitlePlasmodium falciparum profilin
ComponentsPROFILIN
KeywordsPROTEIN BINDING / PROLINE-RICH LIGAND / PLASMODIUM FALCIPARUM / MALARIA / PROFILIN / CYTOSKELETON / ACTIN FILAMENT STRUCTURAL PROTEIN / PROTEIN-BINDING
Function / homology
Function and homology information


cytoplasmic actin-based contraction involved in cell motility / actin monomer binding / phospholipid binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / 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: 2.31 Å
AuthorsKursula, I. / Kursula, P. / Ganter, M. / Panjikar, S. / Matuschewski, K. / Schueler, H.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for Parasite-Specific Functions of the Divergent Profilin of Plasmodium Falciparum
Authors: Kursula, I. / Kursula, P. / Ganter, M. / Panjikar, S. / Matuschewski, K. / Schueler, H.
History
DepositionAug 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN


Theoretical massNumber of molelcules
Total (without water)20,1021
Polymers20,1021
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.440, 50.330, 86.650
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 / CONSERVED PROTEIN


Mass: 20102.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Description: CODONPLUSRIPL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I2J4, UniProt: P86294*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6 / Details: 2.2 M AMMONIUM SULFATE, PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: RH-COATED SI MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→20 Å / Num. obs: 8883 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.8 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / SU B: 17.058 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 446 5 %RANDOM
Rwork0.2 ---
obs0.204 8436 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 83 1420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221363
X-RAY DIFFRACTIONr_bond_other_d0.0010.02885
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9481847
X-RAY DIFFRACTIONr_angle_other_deg1.02732169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.315169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21926.2572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78715226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.726153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8042836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45331335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1074527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2095512
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 30
Rwork0.185 524
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)
14.8104-2.82551.88159.4225-5.59768.97460.02510.12780.51440.0439-0.03850.9478-0.5418-0.45070.01330.13030.023-0.02370.2745-0.06590.2127-14.0514.49810.784
210.4199-1.0657-3.94646.44464.73174.92340.43510.30510.5167-0.5733-0.09230.1345-0.55450.0633-0.34290.13440.0075-0.05040.13530.04290.0718-2.7166.0035.396
324.173119.471115.547315.997212.164710.40951.2402-0.0859-0.43630.2795-1.26972.22591.0816-1.62650.02960.6106-0.08540.07310.5016-0.03010.7742-8.1658.2925.291
412.4063-3.7098-2.89375.00151.09241.3084-0.051-0.29450.66170.18240.2107-0.6299-0.14780.5589-0.15980.1952-0.0212-0.03090.31-0.02510.10226.1894.99414.109
53.0091-6.50361.036715.0585-3.85493.0141-0.0726-0.5101-0.29410.20930.07930.95340.3393-0.2383-0.00680.3128-0.035-0.00920.4441-0.01550.3321.978-10.10511.468
62.5378-0.7963-0.5163.08642.17234.4315-0.0240.1497-0.0587-0.21770.0347-0.315-0.04470.1995-0.01080.0464-0.0168-0.00590.17480.01990.06615.977-5.5384.83
718.153.0362-3.41221.91740.78161.9392-0.20690.4869-1.0194-0.56760.0975-0.13270.1465-0.04220.10940.1865-0.0073-0.01360.24270.00930.1303-9.752-10.936-3.765
83.7268-0.27371.88172.0948-0.51957.5173-0.09010.2410.0533-0.18960.11650.0912-0.1361-0.0109-0.02640.0360.00640.00860.1746-0.01970.0184-6.348-5.1273.209
93.7461-0.05541.76.5997-0.81641.77240.0431-0.4199-0.09620.3489-0.05630.03160.1088-0.37850.01320.02480.00930.00670.1776-0.02690.0067-10.522-6.15811.269
105.3259-9.14553.849916.0888-6.22233.1760.2870.51610.8422-1.0198-0.44730.35220.0815-0.59350.16040.3680.0002-0.01990.3980.00770.4213-17.9085.159-6.616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 23
2X-RAY DIFFRACTION2A24 - 40
3X-RAY DIFFRACTION3A41 - 47
4X-RAY DIFFRACTION4A48 - 62
5X-RAY DIFFRACTION5A63 - 74
6X-RAY DIFFRACTION6A75 - 106
7X-RAY DIFFRACTION7A107 - 112
8X-RAY DIFFRACTION8A113 - 139
9X-RAY DIFFRACTION9A140 - 164
10X-RAY DIFFRACTION10A165 - 174

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