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- PDB-4r1e: Crystal Structure of MTIP from Plasmodium falciparum in complex w... -

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Basic information

Entry
Database: PDB / ID: 4r1e
TitleCrystal Structure of MTIP from Plasmodium falciparum in complex with a peptide-fragment chimera
Components
  • Myosin A tail domain interacting protein
  • Myosin-A
KeywordsPROTEIN BINDING/INHIBITOR / CALMODULIN-LIKE / PROTEIN BINDING / MYOSIN MOTOR / FRAGMENT PEPTIDE / MEMBRANE / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


pellicle / inner membrane pellicle complex / glideosome / myosin complex / myosin II complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin complex / myosin II complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / 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
Chem-3EC / Calmodulin / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Plasmodium falciparum Isolate 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsDouse, C.H. / Vrielink, N. / Cota, E. / Tate, E.W.
CitationJournal: Chemmedchem / Year: 2015
Title: Targeting a Dynamic Protein-Protein Interaction: Fragment Screening against the Malaria Myosin A Motor Complex.
Authors: Douse, C.H. / Vrielink, N. / Wenlin, Z. / Cota, E. / Tate, E.W.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 20, 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 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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
B: Myosin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4253
Polymers18,2392
Non-polymers1851
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-15 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.710, 55.760, 75.860
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


Mass: 16498.234 Da / Num. of mol.: 1 / Fragment: unp residues 61-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: Isolate 3D7 / Gene: MTIP, PFL2225w / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8I4W8
#2: Protein/peptide Myosin-A / PfM-A


Mass: 1741.176 Da / Num. of mol.: 1 / Fragment: unp residues 803-816 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum Isolate 3D7 (eukaryote)
References: UniProt: Q8IDR3
#3: Chemical ChemComp-3EC / 5-{[(2-aminoethyl)sulfanyl]methyl}furan-2-carbaldehyde


Mass: 185.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsGLY802 IS NOT PART OF THE NATURAL SEQUENCE OF THE PROTEIN FROM WHICH THE PEPTIDE IS DERIVED

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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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulfate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: Pilatus 2M / Detector: CCD / Date: Apr 23, 2012
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.98→44.93 Å / Num. all: 11020 / Num. obs: 11020 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.2
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1578 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AOM

4aom


Resolution: 1.98→44.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.664 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22266 1079 9.8 %RANDOM
Rwork0.19578 ---
obs0.19858 9909 96.79 %-
all-10988 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å20 Å2
2---0.42 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.98→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 12 67 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021231
X-RAY DIFFRACTIONr_bond_other_d0.0040.021114
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.961662
X-RAY DIFFRACTIONr_angle_other_deg1.0113.0032550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.64525.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90715202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.313154
X-RAY DIFFRACTIONr_chiral_restr0.0620.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021424
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02279
X-RAY DIFFRACTIONr_mcbond_it0.8751.767630
X-RAY DIFFRACTIONr_mcbond_other0.8561.765629
X-RAY DIFFRACTIONr_mcangle_it1.4652.634784
X-RAY DIFFRACTIONr_mcangle_other1.4662.636785
X-RAY DIFFRACTIONr_scbond_it1.0231.796601
X-RAY DIFFRACTIONr_scbond_other1.0221.799602
X-RAY DIFFRACTIONr_scangle_other1.6592.665879
X-RAY DIFFRACTIONr_long_range_B_refined3.27714.0021450
X-RAY DIFFRACTIONr_long_range_B_other3.19113.9451439
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 74 -
Rwork0.184 735 -
obs--98.3 %

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