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

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Basic information

Entry
Database: PDB / ID: 4mzj
TitleCrystal Structure of MTIP from Plasmodium falciparum in complex with pGly[801,805], a stapled myoA tail peptide
Components
  • Myosin A tail domain interacting protein
  • Myosin-A
KeywordsPROTEIN BINDING/inhibitor / Actomyosin motor / Stapled peptides / PROTEIN BINDING-inhibitor complex
Function / homology
Function and homology information


pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding ...pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin 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, stapled peptide / Myosin A tail domain interacting protein / Myosin-A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.474 Å
AuthorsDouse, C.H. / Garnett, J.A. / Maas, S.J. / Cota, E. / Tate, E.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Crystal Structures of Stapled and Hydrogen Bond Surrogate Peptides Targeting a Fully Buried Protein-Helix Interaction.
Authors: Douse, C.H. / Maas, S.J. / Thomas, J.C. / Garnett, J.A. / Sun, Y. / Cota, E. / Tate, E.W.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Nov 15, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 6, 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: Myosin A tail domain interacting protein
T: Myosin-A


Theoretical massNumber of molelcules
Total (without water)18,6622
Polymers18,6622
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-18 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.380, 53.980, 75.630
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: 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


Type: Oligopeptide / Class: Inhibitor / Mass: 2163.717 Da / Num. of mol.: 1 / Fragment: unp residues 799-816 / Source method: obtained synthetically
Details: Synthesised peptide mimic of Plasmodium falciparum myosin A tail
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IDR3, Myosin-A, stapled peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 801 AND NLE T 805 ARE CYCLIZED ...THE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 801 AND NLE T 805 ARE CYCLIZED THROUGH THEIR SIDE CHAINS AND DOUBLE BOND INVOLVING CE ATOMS. SEE LINK RECORDS

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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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir solution: 20% PEG 3350, 0.2M NaCl, 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: I02 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→37.8 Å / Num. all: 26670 / Num. obs: 26460 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 11.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 33.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.47-1.516.90.862.91860195.6
6.59-37.819.90.02593.9360199.7

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Processing

Software
NameClassification
Adxvdata processing
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4AOM

4aom


Resolution: 1.474→37.8 Å / SU ML: 0.21 / σ(F): 1.11 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1342 5.1 %Random
Rwork0.1798 ---
obs-26404 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.034 Å2 / ksol: 0.332 e/Å3
Refinement stepCycle: LAST / Resolution: 1.474→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 0 154 1416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051316
X-RAY DIFFRACTIONf_angle_d0.9811776
X-RAY DIFFRACTIONf_dihedral_angle_d13.047500
X-RAY DIFFRACTIONf_chiral_restr0.063199
X-RAY DIFFRACTIONf_plane_restr0.004230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4744-1.50280.30511350.30962494X-RAY DIFFRACTION94
1.5028-1.53350.31181060.26872568X-RAY DIFFRACTION97
1.5335-1.56680.25821560.25472637X-RAY DIFFRACTION100
1.5668-1.60330.25421210.22342592X-RAY DIFFRACTION100
1.6033-1.64340.23641390.20932658X-RAY DIFFRACTION100
1.6434-1.68780.20531570.20862648X-RAY DIFFRACTION100
1.6878-1.73750.24011310.19742594X-RAY DIFFRACTION100
1.7375-1.79350.27251450.19672629X-RAY DIFFRACTION100
1.7935-1.85760.19251380.18882639X-RAY DIFFRACTION100
1.8576-1.9320.22871310.17962636X-RAY DIFFRACTION100
1.932-2.01990.20741590.1822595X-RAY DIFFRACTION100
2.0199-2.12640.19981390.17592639X-RAY DIFFRACTION100
2.1264-2.25960.18351630.16812616X-RAY DIFFRACTION100
2.2596-2.43410.19611580.17492626X-RAY DIFFRACTION100
2.4341-2.6790.23781370.18182606X-RAY DIFFRACTION100
2.679-3.06650.20811500.17412613X-RAY DIFFRACTION100
3.0665-3.86280.20431380.15862657X-RAY DIFFRACTION100
3.8628-37.82740.20111250.15782631X-RAY DIFFRACTION100
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)
14.4209-1.00332.10985.0229-0.89635.81760.04710.1124-1.11080.68450.12650.00740.5648-0.2631-0.03780.3573-0.0478-0.00330.2749-0.04250.499114.22-13.82165.986
23.6297-1.0738-1.4823.0670.7435.09610.10550.25270.0133-0.2602-0.0742-0.11020.050.0669-0.03660.12880.0039-0.00850.11280.00890.108820.3316-2.1119-0.3078
35.4474-3.9843-0.66854.8921.58313.0573-0.0255-0.2960.4082-0.01850.1786-0.4166-0.11520.1374-0.1330.1282-0.0182-0.03380.1269-0.01910.15926.9462-0.750413.3993
45.5574-1.4662-0.79933.18060.59535.95430.07330.0369-0.07650.06450.0159-0.07490.24890.2636-0.06970.11910.0077-0.01650.1058-0.00980.126824.7859-6.37035.687
54.1693-2.3882-3.65476.9371.5953.7119-0.3468-0.0079-0.38620.59640.02540.8013-0.0024-0.00740.27460.2188-0.02060.08140.1653-0.03540.26079.6651-4.901615.9521
66.66981.6059-0.25072.04481.25545.966-0.0002-0.1906-0.47460.44220.0591-0.23960.2226-0.0333-0.02930.15290.00790.01040.20150.02580.14783.81586.795122.7105
75.6671-0.32820.01323.7308-0.1131.77410.08-0.05620.12350.04010.03490.0025-0.2254-0.1703-0.12090.16010.01350.00690.1348-0.02290.10296.576916.728818.869
89.02780.22140.33264.4726-0.53453.74370.18130.82540.7651-0.5926-0.09170.2358-0.2363-0.1968-0.07680.30460.0581-0.01350.21840.04650.17625.287917.66537.983
96.1387-1.0042-0.61287.16670.87434.97930.13240.3207-0.296-0.1904-0.13390.5285-0.0035-0.2880.00350.111-0.0254-0.01980.2076-0.01830.1662-0.26188.338913.6524
105.0936-0.37-0.27155.44340.56378.23190.0794-0.0003-0.0050.0561-0.0372-0.0795-0.1624-0.1587-0.02190.09210.00220.00550.0997-0.01990.153711.56476.45914.3785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 63:73)
2X-RAY DIFFRACTION2chain 'A' and (resseq 74:107)
3X-RAY DIFFRACTION3chain 'A' and (resseq 108:118)
4X-RAY DIFFRACTION4chain 'A' and (resseq 119:134)
5X-RAY DIFFRACTION5chain 'A' and (resseq 135:140)
6X-RAY DIFFRACTION6chain 'A' and (resseq 141:151)
7X-RAY DIFFRACTION7chain 'A' and (resseq 152:176)
8X-RAY DIFFRACTION8chain 'A' and (resseq 177:191)
9X-RAY DIFFRACTION9chain 'A' and (resseq 192:204)
10X-RAY DIFFRACTION10chain 'T' and (resseq 799:816)

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