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- PDB-5fx0: Fasciola hepatica calcium binding protein FhCaBP2: Structure of t... -

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Basic information

Entry
Database: PDB / ID: 5fx0
TitleFasciola hepatica calcium binding protein FhCaBP2: Structure of the dynein light chain-like domain. P6422 native.
ComponentsCALCIUM BINDING PROTEIN
KeywordsCELL ADHESION
Function / homology
Function and homology information


dynein complex / microtubule-based process / calcium ion binding
Similarity search - Function
Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calcium binding protein
Similarity search - Component
Biological speciesFASCIOLA HEPATICA (liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNguyen, T.H. / Thomas, C.M. / Timson, D.J. / van Raaij, M.J.
Citation
Journal: Parasitol. Res. / Year: 2016
Title: Fasciola hepatica calcium-binding protein FhCaBP2: structure of the dynein light chain-like domain.
Authors: Nguyen, T.H. / Thomas, C.M. / Timson, D.J. / van Raaij, M.J.
#1: Journal: Parasitology / Year: 2015
Title: Fhcabp2: A Fasciola Hepatica Calcium-Binding Protein with EF-Hand and Dynein Light Chain Domains.
Authors: Thomas, C.M. / Timson, D.J.
History
DepositionFeb 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,5221
Polymers12,5221
Non-polymers00
Water1267
1
A: CALCIUM BINDING PROTEIN

A: CALCIUM BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,0452
Polymers25,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area2190 Å2
ΔGint-14.6 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.630, 59.630, 90.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein CALCIUM BINDING PROTEIN / CALCIUM BINDING PROTEIN FHCABP2


Mass: 12522.271 Da / Num. of mol.: 1 / Fragment: DYNEIN LIGHT CHAIN-LIKE DOMAIN, RESIDUES 99-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FASCIOLA HEPATICA (liver fluke) / Plasmid: PET46EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / Variant (production host): DE3 / References: UniProt: A0A0B5GUS3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES AHHHHHHVDDDDKM ARE AN EXPRESSION TAG.

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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: 1.85 Å3/Da / Density % sol: 33.5 % / Description: NONE
Crystal growpH: 8.5
Details: 10 ML OF 10 MM TRIS-HCL PH 8.5, 50 MM SODIUM CHLORIDE, 20 % (W/V) PEG 3350, 0.2 M SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0047
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015
Details: SI(111) CHANNEL-CUT, CRYOCOOLEDELLIPTICALLY BENT VERTICAL AND HORIZONTAL FOCUSSING MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT, CRYOCOOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0047 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 5253 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FWZ

5fwz


Resolution: 2.3→51.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.251 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27491 484 10.6 %RANDOM
Rwork0.20211 ---
obs0.20938 4093 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.215 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å20 Å2
2--1.8 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→51.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 7 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019838
X-RAY DIFFRACTIONr_bond_other_d0.0020.02773
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9141130
X-RAY DIFFRACTIONr_angle_other_deg0.94431782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.557597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74923.72143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.346155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
X-RAY DIFFRACTIONr_nbd_refined0.180.2276
X-RAY DIFFRACTIONr_nbd_other0.1630.268
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2778
X-RAY DIFFRACTIONr_nbtor_other0.0760.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.228
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8565.82391
X-RAY DIFFRACTIONr_mcbond_other3.8425.814390
X-RAY DIFFRACTIONr_mcangle_it6.1258.71487
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0346.629447
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.959.685642
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 34 -
Rwork0.296 282 -
obs--99.68 %

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