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- PDB-5xgg: Crystal Structure C-terminal SH3 domain of Myosin IB from Entamoe... -

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Basic information

Entry
Database: PDB / ID: 5xgg
TitleCrystal Structure C-terminal SH3 domain of Myosin IB from Entamoeba histolytica
ComponentsUnconventional myosin IB
KeywordsCONTRACTILE PROTEIN / SH3 / MyosinI / Entamoeba histolytica / EhMySH3
Function / homology
Function and homology information


phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium ...phagosome reneutralization / lateral pseudopodium retraction / phagocytic cup lip / regulation of post-lysosomal vacuole size / actin wave / macropinocytic cup cytoskeleton / myosin I complex / chemotaxis to cAMP / pinocytosis / leading edge of lamellipodium / myosin light chain binding / actin-myosin filament sliding / actomyosin / filopodium assembly / endosomal transport / microfilament motor activity / exocytosis / phagocytosis / actin filament organization / filopodium / cell motility / phospholipid binding / phagocytic vesicle membrane / endocytosis / actin filament binding / cell-cell junction / actin cytoskeleton / early endosome / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / SH3 Domains ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Unconventional myosin IB
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGautam, G. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
SERB India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition
Authors: Gautam, G. / Rehman, S.A.A. / Pandey, P. / Gourinath, S.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unconventional myosin IB
B: Unconventional myosin IB
C: Unconventional myosin IB
D: Unconventional myosin IB
E: Unconventional myosin IB
F: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3308
Polymers46,1376
Non-polymers1922
Water11,638646
1
A: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
2
B: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7862
Polymers7,6901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-14 kcal/mol
Surface area4740 Å2
MethodPISA
3
C: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
4
D: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7862
Polymers7,6901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area4720 Å2
MethodPISA
5
E: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4770 Å2
MethodPISA
6
F: Unconventional myosin IB


Theoretical massNumber of molelcules
Total (without water)7,6901
Polymers7,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 77.670, 61.830
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Unconventional myosin IB / Unconventional myosin ib


Mass: 7689.563 Da / Num. of mol.: 6 / Fragment: SH3 domain, UNP residues 995-1049
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: CL6EHI_110810, EHI_110810 / Plasmid: pET-21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4LUC7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.2M ammonium sulphate, 5% v/v isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→77.67 Å / Num. obs: 101866 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.027 / Rsym value: 0.11 / Χ2: 1.94 / Net I/av σ(I): 25.2 / Net I/σ(I): 4.17
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.17 / CC1/2: 0.96 / Rpim(I) all: 0.185 / Rsym value: 0.43 / Χ2: 0.82 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4iim

4iim


Resolution: 1.72→58.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.099 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21878 2512 5.1 %RANDOM
Rwork0.18458 ---
obs0.18627 47114 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.04 Å2
2---0.18 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.72→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 10 649 3720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193156
X-RAY DIFFRACTIONr_bond_other_d0.0020.022888
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9364293
X-RAY DIFFRACTIONr_angle_other_deg1.0436679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4225374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86226.346156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74615521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5341.2011514
X-RAY DIFFRACTIONr_mcbond_other1.5261.21513
X-RAY DIFFRACTIONr_mcangle_it2.2731.791882
X-RAY DIFFRACTIONr_mcangle_other2.2731.7911883
X-RAY DIFFRACTIONr_scbond_it2.8841.5521642
X-RAY DIFFRACTIONr_scbond_other2.881.5491635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3542.1822399
X-RAY DIFFRACTIONr_long_range_B_refined7.76213.364226
X-RAY DIFFRACTIONr_long_range_B_other6.89311.3533751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 170 -
Rwork0.212 3511 -
obs--100 %

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