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- PDB-5xg9: Crystal Structure of PEG-bound SH3 domain of Myosin IB from Entam... -

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Basic information

Entry
Database: PDB / ID: 5xg9
TitleCrystal Structure of PEG-bound SH3 domain of Myosin IB from Entamoeba histolytica
ComponentsUnconventional myosin IB
KeywordsCONTRACTILE PROTEIN / SH3 / MyosinI / Entamoeba histolytica / PEG-bound SH3 complex
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 / vesicle transport along actin filament / microfilament motor activity / endosomal transport / exocytosis / phagocytosis / filopodium / actin filament organization / cell motility / phospholipid binding / endocytosis / phagocytic vesicle membrane / actin filament binding / cell-cell junction / actin cytoskeleton / vesicle / early endosome / ATP binding / plasma membrane / cytosol / cytoplasm
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. / IQ motif, EF-hand binding site ...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. / IQ motif, EF-hand binding site / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / 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
Chem-PG6 / Unconventional myosin IB
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 / 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
B: Unconventional myosin IB
A: Unconventional myosin IB
C: Unconventional myosin IB
D: Unconventional myosin IB
E: Unconventional myosin IB
F: Unconventional myosin IB
G: Unconventional myosin IB
H: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,98819
Polymers61,5178
Non-polymers4,47111
Water10,539585
1
B: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1493
Polymers7,6901
Non-polymers1,4602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4050 Å2
MethodPISA
2
A: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1773
Polymers7,6901
Non-polymers1,4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area4210 Å2
MethodPISA
3
C: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5855
Polymers7,6901
Non-polymers8954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area4140 Å2
MethodPISA
4
D: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9562
Polymers7,6901
Non-polymers2661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4140 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 area4190 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 area3980 Å2
MethodPISA
7
G: Unconventional myosin IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0523
Polymers7,6901
Non-polymers3622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4080 Å2
MethodPISA
8
H: 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 area4080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.462, 79.611, 88.479
Angle α, β, γ (deg.)90.00, 122.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules BACDEFGH

#1: Protein
Unconventional myosin IB / Unconventional myosin ib


Mass: 7689.563 Da / Num. of mol.: 8 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4LUC7

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Non-polymers , 5 types, 596 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000 / Polyethylene glycol


Mass: 1221.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.57 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium sulphate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.78→74.5 Å / Num. obs: 58363 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 17.2
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.84 / Rpim(I) all: 0.28 / Rrim(I) all: 0.55 / Rsym value: 0.471 / Χ2: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGG

5xgg


Resolution: 1.78→74.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.09 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22804 2892 5 %RANDOM
Rwork0.18253 ---
obs0.18485 55453 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.693 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å2-0.95 Å2
2--0.21 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.78→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 149 586 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024014
X-RAY DIFFRACTIONr_bond_other_d0.0020.023797
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9795400
X-RAY DIFFRACTIONr_angle_other_deg1.02738814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3526.957184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
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_it2.3082.2721876
X-RAY DIFFRACTIONr_mcbond_other2.3072.2711875
X-RAY DIFFRACTIONr_mcangle_it3.1813.3812331
X-RAY DIFFRACTIONr_mcangle_other3.1813.3822332
X-RAY DIFFRACTIONr_scbond_it3.9862.832136
X-RAY DIFFRACTIONr_scbond_other3.9852.832136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7684.0073069
X-RAY DIFFRACTIONr_long_range_B_refined8.04620.9264879
X-RAY DIFFRACTIONr_long_range_B_other8.04520.9324880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.783→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 183 -
Rwork0.226 3817 -
obs--91.39 %

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