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- PDB-2qac: The closed MTIP-MyosinA-tail complex from the malaria parasite in... -

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Basic information

Entry
Database: PDB / ID: 2qac
TitleThe closed MTIP-MyosinA-tail complex from the malaria parasite invasion machinery
Components
  • Myosin A tail domain interacting protein MTIP
  • Myosin-A
KeywordsMEMBRANE PROTEIN / Malaria Invasion / Structural Genomics / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding ...glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / EF-hand domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin-A / Myosin A tail domain interacting protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsBosch, J. / Turley, S. / Roach, C.M. / Daly, T.M. / Bergman, L.W. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Closed MTIP-Myosin A-Tail Complex from the Malaria Parasite Invasion Machinery.
Authors: Bosch, J. / Turley, S. / Roach, C.M. / Daly, T.M. / Bergman, L.W. / Hol, W.G.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin A tail domain interacting protein MTIP
T: Myosin-A


Theoretical massNumber of molelcules
Total (without water)18,5452
Polymers18,5452
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.217, 54.120, 76.326
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 Myosin A tail domain interacting protein MTIP


Mass: 16701.496 Da / Num. of mol.: 1 / Fragment: Residues 61-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFL2225w / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q8I4W8
#2: Protein/peptide Myosin-A


Mass: 1843.290 Da / Num. of mol.: 1 / Fragment: C-terminal tail, residues 803-817 / Source method: obtained synthetically
Details: Synthetic peptide containing the C-terminal residues of Plasmodium yoelii Myosin A, UNP entry Q7RQ71, MYOA_PLAYO, sequence position 803-817
References: UniProt: Q7RQ71
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M KNO3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.98
SYNCHROTRONSSRL BL9-220.97890, 0.97930, 0.90500
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 20, 2006
ADSC QUANTUM 3152CCDApr 22, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97891
30.97931
40.9051
ReflectionResolution: 1.7→20 Å / Num. all: 14110 / Num. obs: 14110 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.26 Å2 / Rsym value: 0.055 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.791 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1073 / Rsym value: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.127 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22828 739 5 %RANDOM
Rwork0.16694 ---
obs0.16984 14109 100 %-
all-14110 --
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: 16.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 228 1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221357
X-RAY DIFFRACTIONr_bond_other_d0.0010.02914
X-RAY DIFFRACTIONr_angle_refined_deg0.9421.971841
X-RAY DIFFRACTIONr_angle_other_deg0.83632258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.895176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74625.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5915264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.643156
X-RAY DIFFRACTIONr_chiral_restr0.0580.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
X-RAY DIFFRACTIONr_nbd_refined0.1920.2358
X-RAY DIFFRACTIONr_nbd_other0.1750.21010
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2665
X-RAY DIFFRACTIONr_nbtor_other0.0810.2683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.55241086
X-RAY DIFFRACTIONr_mcbond_other0.3024334
X-RAY DIFFRACTIONr_mcangle_it1.80561334
X-RAY DIFFRACTIONr_scbond_it2.2776623
X-RAY DIFFRACTIONr_scangle_it3.28410497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.791 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.28 64 -
Rwork0.224 1073 -
obs--100 %
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)
117.2754-3.487411.6731.1079-1.82598.58420.79910.5593-1.9313-1.24350.00430.04911.41830.9252-0.80330.27730.122-0.099-0.04890.01530.1782-16.8452-15.2538-8.1764
29.0443-1.9552-2.760814.77988.901233.32910.3584-0.3768-0.57160.3212-0.1608-0.53721.4591.6457-0.19760.09640.1897-0.10580.08480.01850.0504-12.7691-10.6980.4853
30.86890.35880.00790.9511-0.17632.08220.0456-0.04490.02280.0788-0.01890.0287-0.0069-0.0161-0.02670.0770.00230.00120.05280.00270.0685-21.3025-1.1919-2.5684
43.0591-0.09161.14220.0612-0.49834.10980.1941-0.0590.0653-0.0102-0.01030.09260.2546-0.246-0.18380.0792-0.0237-0.02270.05610.04230.0967-29.3127-4.705-7.16
52.43080.5354-1.70360.2166-0.67152.08340.08310.0847-0.2624-0.056-0.0611-0.20320.1139-0.1008-0.0220.09740.00530.01820.0367-0.00430.1051-17.0927-6.2808-10.6855
61.8552-0.37840.34371.4509-0.84652.0496-0.13720.2367-0.1441-0.09460.14380.0881-0.03870.0311-0.00660.0637-0.00350.0190.09840.00290.0541-2.49459.4277-24.1777
71.79880.30480.05641.4254-0.06270.56640.0779-0.00580.21480.1146-0.00380.0539-0.0690.0209-0.07410.075-0.01480.0010.05210.02240.0762-7.164817.032-14.0656
81.72340.8588-0.51763.1632-0.33940.99630.0526-0.0105-0.10980.1462-0.0164-0.3335-0.1279-0.0501-0.03620.04260.0163-0.00590.08410.03010.09510.53249.9123-13.6021
90.14180.1565-0.60062.5179-0.54632.54850.05330.1024-0.02870.054-0.105-0.03950.00340.00840.05170.05480.00020.00360.07970.01340.0828-11.95646.2308-14.5075
1016.5457-4.6835-7.68789.363415.940927.1449-0.2367-0.7043-0.0760.0580.12310.04130.26120.75270.11360.1331-0.034-0.04120.04180.01290.0626-9.28786.0796-3.7786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA61 - 703 - 12
2X-RAY DIFFRACTION2AA71 - 7613 - 18
3X-RAY DIFFRACTION3AA77 - 11319 - 55
4X-RAY DIFFRACTION4AA114 - 12556 - 67
5X-RAY DIFFRACTION5AA126 - 14068 - 82
6X-RAY DIFFRACTION6AA141 - 15583 - 97
7X-RAY DIFFRACTION7AA156 - 18998 - 131
8X-RAY DIFFRACTION8AA190 - 204132 - 146
9X-RAY DIFFRACTION9TB803 - 8121 - 10
10X-RAY DIFFRACTION10TB813 - 81711 - 15

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