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- PDB-7ekz: Structural and functional insights into Hydra Actinoporin-Like To... -

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Basic information

Entry
Database: PDB / ID: 7ekz
TitleStructural and functional insights into Hydra Actinoporin-Like Toxin 1 (HALT-1)
ComponentsHALT-1
KeywordsTOXIN / Hydra / actinoporin / HALT-1 / pore forming toxin
Function / homologyFORMIC ACID
Function and homology information
Biological speciesHydra vulgaris (swiftwater hydra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsKer, D.S. / Sha, X.H. / Jonet, M.A. / Hwang, J.S. / Ng, C.L.
Funding support Malaysia, 2items
OrganizationGrant numberCountry
Universiti Kebangsaan MalaysiaGP-2019-K019584 Malaysia
Universiti Kebangsaan MalaysiaGP-2020-K019584 Malaysia
CitationJournal: Sci Rep / Year: 2021
Title: Structural and functional analysis of Hydra Actinoporin-Like Toxin 1 (HALT-1).
Authors: Ker, D.S. / Sha, H.X. / Jonet, M.A. / Hwang, J.S. / Ng, C.L.
History
DepositionApr 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1737
Polymers20,7581
Non-polymers4146
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The recombinant protein of HALT-1 was eluted with the estimated size of ~11kDa using HiLoad Superdex 75 PG 16/600 (GE Healthcare). The eluted protein was shown with size of ...Evidence: gel filtration, The recombinant protein of HALT-1 was eluted with the estimated size of ~11kDa using HiLoad Superdex 75 PG 16/600 (GE Healthcare). The eluted protein was shown with size of ~22kDA in the SDS-PAGE suggests that, the protein is likely a monomer in the solution. It is not known why the protein was eluted with smaller size compared to the estimated size.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-0 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.100, 49.590, 77.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HALT-1


Mass: 20758.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami 2 (DE3)
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium formate, 22% w/v polyethylene glycol 3550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.43→23.55 Å / Num. obs: 33402 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.068 / Rrim(I) all: 0.163 / Net I/σ(I): 5.2
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2 / Num. unique obs: 1577 / CC1/2: 0.774 / Rpim(I) all: 0.276 / Rrim(I) all: 0.506 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWY

1gwy


Resolution: 1.43→23.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.009 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1702 5.2 %RANDOM
Rwork0.1628 ---
obs0.1658 30818 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.23 Å2 / Biso mean: 11.024 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--0.72 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.43→23.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 27 345 1655
Biso mean--26.87 34.31 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191405
X-RAY DIFFRACTIONr_bond_other_d0.0020.021340
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.941906
X-RAY DIFFRACTIONr_angle_other_deg0.96833095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33124.10756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39215232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.929154
X-RAY DIFFRACTIONr_chiral_restr0.1170.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021603
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02335
X-RAY DIFFRACTIONr_rigid_bond_restr3.87132745
X-RAY DIFFRACTIONr_sphericity_free93.649565
X-RAY DIFFRACTIONr_sphericity_bonded20.48352987
LS refinement shellResolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 103 -
Rwork0.209 2219 -
all-2322 -
obs--94.12 %
Refinement TLS params.Method: refined / Origin x: 2.2179 Å / Origin y: -15.9493 Å / Origin z: -11.4596 Å
111213212223313233
T0.0141 Å2-0.0007 Å2-0.0002 Å2-0.0007 Å2-0.0009 Å2--0.0024 Å2
L0.1051 °2-0.0286 °2-0.0059 °2-0.0469 °2-0.0028 °2--0.0463 °2
S0.0005 Å °0.0059 Å °-0.0003 Å °-0.0003 Å °-0.0001 Å °-0.0013 Å °-0.0006 Å °0 Å °-0.0003 Å °

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