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

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Basic information

Entry
Database: PDB / ID: 5fwz
TitleFasciola hepatica calcium binding protein FhCaBP2: Structure of the dynein light chain-like domain. P41212 mercury derivative.
ComponentsCALCIUM BINDING PROTEIN
KeywordsCALCIUM-BINDING PROTEIN
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 / SAD / 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7604
Polymers11,4881
Non-polymers2713
Water1,02757
1
A: CALCIUM BINDING PROTEIN
hetero molecules

A: CALCIUM BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5198
Polymers22,9762
Non-polymers5436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3110 Å2
ΔGint-113 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 59.880, 81.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 11488.179 Da / Num. of mol.: 1 / Fragment: DYNEIN LIGHT CHAIN-LIKE DOMAIN, RESIDUES 92-189
Source method: isolated from a genetically manipulated source
Details: THE PURIFIED PROTEIN CONTAIN ALSO THE N- TERMINAL HIS-TAG AND EF-HAND DOMAIN, HOWEVER WE BELIEVE THIS WAS PROTEOLYSED IN SITU IN THE CRYSTALLIZATION DROP. THEREFORE ONLY OBSERVED RESIDUES ...Details: THE PURIFIED PROTEIN CONTAIN ALSO THE N- TERMINAL HIS-TAG AND EF-HAND DOMAIN, HOWEVER WE BELIEVE THIS WAS PROTEOLYSED IN SITU IN THE CRYSTALLIZATION DROP. THEREFORE ONLY OBSERVED RESIDUES ARE GIVEN. FOR MORE DETAILS SEE THE PRIMARY REFERENCE.
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: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.2 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growpH: 8.5
Details: 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: 1.0056
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015
Details: ELLIPTICALLY 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: 1.0056 Å / Relative weight: 1
ReflectionResolution: 2.3→23 Å / Num. obs: 7026 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→22.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.264 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24051 702 10 %RANDOM
Rwork0.19132 ---
obs0.1965 6289 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.662 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--1.12 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→22.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms799 0 3 57 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019824
X-RAY DIFFRACTIONr_bond_other_d0.0020.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9271115
X-RAY DIFFRACTIONr_angle_other_deg0.94831773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.042598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92223.07739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16415148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.187156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined0.2090.2404
X-RAY DIFFRACTIONr_nbd_other0.1490.21466
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2780
X-RAY DIFFRACTIONr_nbtor_other0.0790.2862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0940.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6683.426389
X-RAY DIFFRACTIONr_mcbond_other2.673.42388
X-RAY DIFFRACTIONr_mcangle_it4.5315.119485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9883.888435
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0035.687629
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→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 44 -
Rwork0.23 445 -
obs--100 %

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