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

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Basic information

Entry
Database: PDB / ID: 4mzk
TitleCrystal Structure of MTIP from Plasmodium falciparum in complex with pGly[807,811], a stapled myoA tail peptide
Components
  • Myosin A tail domain interacting protein
  • pGly[807,811], a stapled myoA tail peptide
KeywordsPROTEIN BINDING/inhibitor / Actomyosin motor / Stapled peptides / PROTEIN BINDING-inhibitor complex
Function / homology
Function and homology information


pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton ...pellicle / inner membrane pellicle complex / glideosome / myosin II complex / myosin 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 ...: / 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
pGly[807,811], a stapled myoA tail 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: 1.82 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: pGly[807,811], a stapled myoA tail peptide


Theoretical massNumber of molelcules
Total (without water)18,6762
Polymers18,6762
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.980, 55.030, 75.830
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 pGly[807,811], a stapled myoA tail peptide / PfM-A


Type: Peptide-like / Class: Inhibitor / Mass: 2177.744 Da / Num. of mol.: 1 / Fragment: unp residues 799-816 / Source method: obtained synthetically
Details: Synthesised peptide mimic of Plasmodium falciparum myosin A tail using Fmoc-Solid Phase Peptide Synthesis
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8IDR3, pGly[807,811], a stapled myoA tail peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 807 AND NLE T 811 ARE CYCLIZED ...THE PEPTIDE CORRESPONDING TO CHAIN T IS A STAPLED PEPTIDE. THE NLE T 807 AND NLE T 811 ARE CYCLIZED THROUGH THEIR SIDE CHAINS AND A 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir solution: 200 mM ammonium acetate, 10 mM magnesium acetate, 50 mM sodium cacodylate trihydrate, 30 % PEG 8000, pH 6.5, 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: 1.82→37.98 Å / Num. all: 14866 / Num. obs: 14865 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.82-1.8713.40.783.81057199.9
8.14-37.989.90.02477209199.3

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4AOM

4aom


Resolution: 1.82→37.915 Å / SU ML: 0.26 / σ(F): 1.49 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 754 5.08 %Random
Rwork0.18 ---
obs-14820 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.279 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 1.82→37.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 0 101 1353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071281
X-RAY DIFFRACTIONf_angle_d1.021727
X-RAY DIFFRACTIONf_dihedral_angle_d12.606474
X-RAY DIFFRACTIONf_chiral_restr0.071196
X-RAY DIFFRACTIONf_plane_restr0.003222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.88510.32281260.2722611X-RAY DIFFRACTION100
1.8851-1.96050.31510.21762601X-RAY DIFFRACTION100
1.9605-2.04980.22421500.19332610X-RAY DIFFRACTION100
2.0498-2.15780.25241590.19082597X-RAY DIFFRACTION100
2.1578-2.2930.23981350.18022625X-RAY DIFFRACTION100
2.293-2.470.26121350.18262622X-RAY DIFFRACTION100
2.47-2.71850.18951560.1812577X-RAY DIFFRACTION100
2.7185-3.11170.21331350.18152613X-RAY DIFFRACTION100
3.1117-3.91980.21781270.16752640X-RAY DIFFRACTION100
3.9198-37.92320.19511250.16442628X-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)
15.1399-0.98251.63494.1463-1.20723.4345-0.25690.2871-1.19570.60120.15370.13930.8085-0.259-0.06270.4579-0.07410.05670.3378-0.00690.454114.5737-14.11835.4728
24.39061.9734-0.16143.7046-0.32772.5582-0.10250.295-0.2201-0.52870.047-0.19440.29490.07560.06550.21230.00560.0030.1491-0.01910.129521.5776-5.6423-4.9436
34.3272-0.0661-0.27462.53130.04223.3218-0.1182-0.03680.3616-0.12010.1168-0.0527-0.273-0.0423-0.0420.15580.00590.01070.12980.00310.150821.39580.83742.0621
42.1782-0.77030.4541.04310.49751.693-0.1537-0.2070.19860.14920.0344-0.03590.0562-0.06030.11070.15050.0066-0.02350.115-0.01140.153123.5421-1.548911.385
53.6842-0.225-0.19731.9129-0.06283.17290.15130.054-0.187-0.02810.0411-0.13550.36970.2201-0.18060.18250.0243-0.00160.134-0.00490.148724.7958-7.80695.3112
65.2007-0.8398-2.88871.88270.85362.1633-0.13520.0443-0.54990.2087-0.13620.31250.1478-0.17890.31230.1436-0.0040.02820.15780.01320.315610.5748-5.173815.1657
73.40960.48140.40044.22890.08913.7865-0.0793-0.3344-0.49020.35420.0171-0.16310.29820.16520.11040.1462-0.00870.02750.21210.01050.15754.04927.264622.4164
84.0325-1.55344.21392.2427-1.89584.4511-0.0172-1.716-0.13611.0720.47830.0554-0.1062-0.0046-0.18080.29650.06580.05240.5082-0.02980.2769-2.768315.924426.641
91.82560.1273-0.38510.87530.25831.04210.0290.01440.2592-0.0560.029-0.0802-0.1512-0.0202-0.00080.20850.01690.05510.1633-0.03250.20648.890516.716216.9435
104.64870.43730.69533.34810.50111.4948-0.13190.92720.6919-0.71220.36230.20350.0029-0.6820.15180.34470.01840.00320.38740.13310.19415.12417.24797.7005
113.98430.0157-0.34364.8351-0.49453.46930.00980.4546-0.2628-0.4454-0.07570.47130.232-0.3730.06580.1515-0.0319-0.03370.2209-0.03220.193-0.79868.498313.6789
123.88370.0181-0.07363.712-0.21125.80570.1343-0.0669-0.04040.03040.05380.1877-0.2371-0.1449-0.16650.11460.02140.02470.12310.00110.166111.76166.224714.535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 63:73 )A63 - 73
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:88 )A74 - 88
3X-RAY DIFFRACTION3( CHAIN A AND RESID 89:101 )A89 - 101
4X-RAY DIFFRACTION4( CHAIN A AND RESID 102:120 )A102 - 120
5X-RAY DIFFRACTION5( CHAIN A AND RESID 121:133 )A121 - 133
6X-RAY DIFFRACTION6( CHAIN A AND RESID 134:140 )A134 - 140
7X-RAY DIFFRACTION7( CHAIN A AND RESID 141:151 )A141 - 151
8X-RAY DIFFRACTION8( CHAIN A AND RESID 152:157 )A152 - 157
9X-RAY DIFFRACTION9( CHAIN A AND RESID 158:176 )A158 - 176
10X-RAY DIFFRACTION10( CHAIN A AND RESID 177:191 )A177 - 191
11X-RAY DIFFRACTION11( CHAIN A AND RESID 192:204 )A192 - 204
12X-RAY DIFFRACTION12( CHAIN T AND RESID 799:816 )T799 - 816

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