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- PDB-3nec: Crystal Structure of Toxoplasma gondii Profilin -

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Basic information

Entry
Database: PDB / ID: 3nec
TitleCrystal Structure of Toxoplasma gondii Profilin
ComponentsInflammatory profilin
KeywordsACTIN-BINDING PROTEIN / actin-binding / profilin
Function / homology
Function and homology information


cytoplasmic actin-based contraction involved in cell motility / actin monomer binding / phospholipid binding / actin cytoskeleton / 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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Profilin
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKucera, K. / Modis, Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure-based analysis of Toxoplasma gondii profilin: a parasite-specific motif is required for recognition by Toll-like receptor 11.
Authors: Kucera, K. / Koblansky, A.A. / Saunders, L.P. / Frederick, K.B. / De La Cruz, E.M. / Ghosh, S. / Modis, Y.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inflammatory profilin
B: Inflammatory profilin
C: Inflammatory profilin
D: Inflammatory profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,79812
Polymers71,7974
Non-polymers1,0018
Water13,565753
1
A: Inflammatory profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2003
Polymers17,9491
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inflammatory profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2003
Polymers17,9491
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Inflammatory profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3544
Polymers17,9491
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Inflammatory profilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0452
Polymers17,9491
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.528, 53.335, 68.617
Angle α, β, γ (deg.)74.70, 73.82, 68.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Inflammatory profilin / Profilin


Mass: 17949.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal 6x Histidine tag and thrombin cleavage sequence.
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: PRF / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q58NA1
#2: Chemical
ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.4 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3:3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→27 Å / Num. obs: 61203 / % possible obs: 94 % / Redundancy: 3.8 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.18
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 69.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JKF without residues 57-77

2jkf


Resolution: 1.7→26.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.801 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19618 2814 4.4 %RANDOM
Rwork0.1587 ---
obs-61203 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.27 Å2-0.1 Å2
2--0.03 Å2-0.04 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.107 Å0.011 Å
Luzzati sigma a-0.072 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 52 753 5779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215198
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.9437058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98325.992247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01615827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.591512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024042
X-RAY DIFFRACTIONr_mcbond_it2.33653277
X-RAY DIFFRACTIONr_mcangle_it3.633105215
X-RAY DIFFRACTIONr_scbond_it7.634201921
X-RAY DIFFRACTIONr_scangle_it10.768251828
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 19 -
Rwork0.23446 3362 -
obs-7550 77.24 %
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)
10.901-0.14770.38530.97910.33081.07120.0266-0.02570.05860.0312-0.02560.00080.09210.019-0.0010.0457-0.01540.03180.04820.01240.072-0.3893-0.77499.2715
22.1073-1.39650.88441.0635-0.40340.6136-0.00720.03120.01340.13360.01830.0863-0.0179-0.0313-0.0110.1009-0.02970.01930.07410.00180.1261-19.1563-8.5841-2.3137
31.56670.03210.17391.03730.15831.0501-0.03080.00030.2037-0.0168-0.00520.0276-0.07080.01570.0360.0278-0.01350.01210.03670.01760.08239.5277-29.15731.2017
41.66083.4962-1.60086.1629-3.05831.43150.24280.03350.22390.2107-0.1250.3507-0.2480.0424-0.11780.1293-0.07910.01830.14960.01180.152128.0863-16.509512.5058
50.5114-0.21170.20480.8198-0.20831.44540.05080.0821-0.0567-0.0819-0.0570.01720.14140.14040.00620.07410.0203-0.01170.0746-0.01270.0721-9.8091-14.6555-21.6205
61.9009-2.2835-0.2772.43110.19410.9337-0.0029-0.0768-0.11480.03050.0109-0.1050.13830.2479-0.00790.12120.02280.00240.18890.01220.1337-0.8543-13.0485-43.2061
70.7053-0.09860.07850.7269-0.04372.2928-0.06940.00720.01320.0025-0.0382-0.04730.0431-0.02130.10750.07190.00520.00070.0503-0.00950.06316.473-39.0618-31.8902
80.2835-1.64580.43685.6214-0.80630.88160.03710.0843-0.115-0.0331-0.05620.08310.0098-0.09550.01910.0698-0.0190.01220.1096-0.02280.10940.1408-45.7232-10.3199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 48
2X-RAY DIFFRACTION1A68 - 163
3X-RAY DIFFRACTION2A49 - 67
4X-RAY DIFFRACTION3B3 - 48
5X-RAY DIFFRACTION3B68 - 163
6X-RAY DIFFRACTION4B49 - 67
7X-RAY DIFFRACTION5C3 - 48
8X-RAY DIFFRACTION5C68 - 163
9X-RAY DIFFRACTION6C49 - 67
10X-RAY DIFFRACTION7D3 - 48
11X-RAY DIFFRACTION7D68 - 163
12X-RAY DIFFRACTION8D49 - 67

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