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- PDB-4aom: MTIP and MyoA complex -

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Basic information

Entry
Database: PDB / ID: 4aom
TitleMTIP and MyoA complex
Components
  • MYOSIN A TAIL DOMAIN INTERACTING PROTEIN
  • MYOSIN-A
KeywordsMEMBRANE PROTEIN/MOTOR PROTEIN / MEMBRANE PROTEIN-MOTOR PROTEIN COMPLEX
Function / homology
Function and homology information


pellicle / 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 / cytoskeletal motor activity ...pellicle / 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 / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / membrane / 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 tail domain interacting protein / Myosin-A / Myosin-A
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsSalgado, P.S. / Douse, C.H. / Simpson, P.J. / Thomas, J.C. / Holder, A.A. / Tate, E.W. / Cota, E.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Regulation of the Plasmodium Motor Complex: Phosphorylation of Myosin a Tail Interacting Protein (Mtip) Loosens its Grip on Myoa
Authors: Douse, C.H. / Green, J.L. / Salgado, P.S. / Simpson, P.J. / Thomas, J.C. / Holder, A.A. / Tate, E.W. / Cota, E.
History
DepositionMar 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 13, 2013Group: Database references / Structure summary
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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: MYOSIN A TAIL DOMAIN INTERACTING PROTEIN
T: MYOSIN-A


Theoretical massNumber of molelcules
Total (without water)18,8392
Polymers18,8392
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-16.3 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.264, 54.704, 75.024
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: MYOSIN-A INTERACTING DOMAIN, RESIDUES 60-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8I4W8
#2: Protein/peptide MYOSIN-A / PFM-A / MYOA


Mass: 2137.680 Da / Num. of mol.: 1 / Fragment: TAIL, RESIDUES 799-816 / Source method: obtained synthetically / Details: N-TERMINAL ACETYLATED
Source: (synth.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
References: UniProt: Q9UAR6, UniProt: Q8IDR3*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.36 Å3/Da / Density % sol: 47.8 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2M POTASSIUM THIOCYANATE, 20% PEG3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.94→13.91 Å / Num. obs: 11754 / % possible obs: 98.7 % / Observed criterion σ(I): 5.4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 10.8
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.4 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QAC

2qac


Resolution: 1.939→13.218 Å / SU ML: 0.19 / σ(F): 1.12 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 562 4.8 %
Rwork0.1766 --
obs0.1788 11676 98.43 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.249 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2299 Å20 Å20 Å2
2---0.0141 Å20 Å2
3----0.2159 Å2
Refinement stepCycle: LAST / Resolution: 1.939→13.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 215 1511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071314
X-RAY DIFFRACTIONf_angle_d0.9681769
X-RAY DIFFRACTIONf_dihedral_angle_d13.217497
X-RAY DIFFRACTIONf_chiral_restr0.064198
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9386-2.13290.26141480.18112647X-RAY DIFFRACTION96
2.1329-2.43990.23621400.16742746X-RAY DIFFRACTION98
2.4399-3.06770.20731330.17922784X-RAY DIFFRACTION99
3.0677-13.21870.21161410.17782937X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.7346 Å / Origin y: -3.5085 Å / Origin z: 10.5338 Å
111213212223313233
T0.0248 Å20.0049 Å2-0.0033 Å2-0.0328 Å20.0067 Å2--0.0323 Å2
L0.1864 °2-0.1413 °20.1225 °2-0.2313 °2-0.0964 °2--0.3808 °2
S-0.0011 Å °0.0084 Å °0.0356 Å °-0.0406 Å °-0.0054 Å °-0.0178 Å °0.0078 Å °0.0559 Å °0.0028 Å °
Refinement TLS groupSelection details: ALL

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