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- PDB-5x2e: Crystal structure of Calmodulin like domain of CsTAL3 (1-81aa) -

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Basic information

Entry
Database: PDB / ID: 5x2e
TitleCrystal structure of Calmodulin like domain of CsTAL3 (1-81aa)
ComponentsTegumental protein 20.8 kDa
KeywordsCELL ADHESION / Calcium-binding protein / CsTAL3 / Calmodulin / Clonorchis sinensis
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 superfamily / Dynein light chain type 1 / 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
Tegumental protein 20.8 kDa
Similarity search - Component
Biological speciesClonorchis sinensis (oriental liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å
AuthorsJo, C.H. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2013R1A1A2008404 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis
Authors: Jo, C.H. / Son, J. / Kim, S. / Oda, T. / Kim, J. / Lee, M.R. / Sato, M. / Kim, H.T. / Unzai, S. / Park, S.Y. / Hwang, K.Y.
History
DepositionJan 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tegumental protein 20.8 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0842
Polymers9,0441
Non-polymers401
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area5140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.827, 47.827, 42.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Tegumental protein 20.8 kDa / CsTAL3


Mass: 9044.101 Da / Num. of mol.: 1 / Fragment: Calmodulin domain, UNP residues 2-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clonorchis sinensis (oriental liver fluke)
Production host: Escherichia coli (E. coli) / References: UniProt: Q2PMV7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 90 mM sodium acetate, 3.25 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 23678 / % possible obs: 99.6 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.01 / Rrim(I) all: 0.035 / Χ2: 0.557 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.326.50.3920.7390.1580.4240.28999.4
1.32-1.357.10.3660.7970.1410.3940.29699.6
1.35-1.377.10.3190.8690.1220.3430.31899.8
1.37-1.48.30.2930.9150.1030.3110.35299.8
1.4-1.438.40.2640.9560.0930.280.34999.7
1.43-1.468.50.220.9640.0770.2330.37799.5
1.46-1.59.80.1820.9810.0590.1920.407100
1.5-1.54100.1530.9880.0490.1610.434100
1.54-1.59100.1270.9920.0410.1340.45199.8
1.59-1.6410.30.0990.9950.0310.1040.47599.9
1.64-1.711.20.0830.9970.0250.0860.495100
1.7-1.7611.10.0660.9980.020.070.52299.7
1.76-1.84120.0560.9990.0160.0590.56999.9
1.84-1.9412.50.0480.9990.0140.050.588100
1.94-2.0611.90.0390.9990.0120.0410.699.8
2.06-2.2213.10.0340.9990.010.0360.63100
2.22-2.4512.40.0310.9990.0090.0330.68799.9
2.45-2.813.40.030.9990.0090.0320.723100
2.8-3.5312.70.0290.9990.0080.030.82899.4
3.53-5012.40.0310.9990.0090.0321.03195.4

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD structure

Resolution: 1.299→47.827 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 2022 8.55 %
Rwork0.1801 --
obs0.1831 23657 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.299→47.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 1 112 749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011649
X-RAY DIFFRACTIONf_angle_d1.285879
X-RAY DIFFRACTIONf_dihedral_angle_d14.308240
X-RAY DIFFRACTIONf_chiral_restr0.04998
X-RAY DIFFRACTIONf_plane_restr0.009115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2992-1.33160.30121430.25151534X-RAY DIFFRACTION99
1.3316-1.36770.26171400.22541536X-RAY DIFFRACTION100
1.3677-1.40790.23381450.20121528X-RAY DIFFRACTION100
1.4079-1.45330.24871440.17551549X-RAY DIFFRACTION99
1.4533-1.50530.22151410.15751533X-RAY DIFFRACTION100
1.5053-1.56560.20181430.15351558X-RAY DIFFRACTION100
1.5656-1.63680.22021450.15541528X-RAY DIFFRACTION100
1.6368-1.72310.18351480.15371539X-RAY DIFFRACTION100
1.7231-1.83110.2271430.1551564X-RAY DIFFRACTION100
1.8311-1.97250.22971420.16611535X-RAY DIFFRACTION100
1.9725-2.1710.19851470.16241578X-RAY DIFFRACTION100
2.171-2.48510.18671450.16581550X-RAY DIFFRACTION100
2.4851-3.13090.24921450.20111554X-RAY DIFFRACTION100
3.1309-47.85940.20781510.18831549X-RAY DIFFRACTION97

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