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- PDB-5cx2: Structure of coiled coil domain of Leishmania donovani coronin -

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Basic information

Entry
Database: PDB / ID: 5cx2
TitleStructure of coiled coil domain of Leishmania donovani coronin
Components(Coronin) x 4
KeywordsSTRUCTURAL PROTEIN / 4 helix bundle / antiparallel coiled coils
Function / homology
Function and homology information


actin filament organization / actin filament binding / ribosome
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsNayak, A.R. / Karade, S.S. / Srivastava, V.K. / Pratap, J.V.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of Leishmania donovani coronin coiled coil domain reveals an antiparallel 4 helix bundle with inherent asymmetry
Authors: Nayak, A.R. / Karade, S.S. / Srivastava, V.K. / Rana, A.K. / Gupta, C.M. / Sahasrabuddhe, A.A. / Pratap, J.V.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coronin
B: Coronin
C: Coronin
D: Coronin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0108
Polymers24,7284
Non-polymers2824
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.390, 48.780, 45.350
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A456 - 505
2114B456 - 505
3114C456 - 505
4114D456 - 505

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.32655, 0.042245, -0.944235), (0.047337, -0.997016, -0.060977), (-0.943994, -0.064609, 0.323576)75.546013, 70.575592, 57.53574
3given(-0.221862, -0.754139, 0.618103), (-0.885119, -0.110179, -0.452133), (0.409073, -0.647406, -0.643059)81.271858, 92.117188, 17.054779
4given(-0.452231, 0.787155, 0.419373), (0.786038, 0.129556, 0.604449), (0.421463, 0.602994, -0.677323)43.592731, -17.40983, -25.57036

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coronin


Mass: 6826.225 Da / Num. of mol.: 1 / Fragment: UNP residues 459-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plysS / References: UniProt: Q3T1U8

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Protein/peptide , 3 types, 3 molecules BCD

#2: Protein/peptide Coronin


Mass: 5937.615 Da / Num. of mol.: 1 / Fragment: UNP residues 462-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plysS / References: UniProt: Q3T1U8
#3: Protein/peptide Coronin


Mass: 6038.719 Da / Num. of mol.: 1 / Fragment: UNP residues 461-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plysS / References: UniProt: Q3T1U8
#4: Protein/peptide Coronin


Mass: 5925.562 Da / Num. of mol.: 1 / Fragment: UNP residues 461-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plysS / References: UniProt: Q3T1U8

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Non-polymers , 3 types, 93 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 52.22 % / Description: Plates
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 3 ul of 8 mg/ml purified protein + 3 ul of reservoir solution (0.85M Ammonium Sulphate, 0.8M Lithium Sulphate, 10mM Sodium Citrate) equilibrated against 1ml reservoir. Crystals appeared in 7 - 10 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 14275 / % possible obs: 87.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.118 / Χ2: 1.058 / Net I/av σ(I): 12.143 / Net I/σ(I): 6.9 / Num. measured all: 90732
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.97-2.043.56610.77140.8
2.04-2.124.19511.16158.7
2.12-2.224.412480.81677.10.718
2.22-2.345.215481.23795.20.627
2.34-2.486.416140.91599.90.474
2.48-2.677.116521.0181000.394
2.67-2.947.416141.1731000.262
2.94-3.377.516371.0741000.148
3.37-4.247.516511.0851000.094
4.24-507.316991.0611000.075

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.21→42.35 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.883 / SU B: 22.844 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28885 589 5.1 %RANDOM
Rwork0.23293 ---
obs0.23603 10966 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: 40.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0 Å21.03 Å2
2--0.66 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.21→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 17 89 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9832152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6885199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60326.42984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12715306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.5611511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021178
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.7763.678808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.8845.4811003
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.5674.308799
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.14535.1346668
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr14.70131607
X-RAY DIFFRACTIONr_sphericity_free26.584532
X-RAY DIFFRACTIONr_sphericity_bonded35.56851665
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 244 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional1.160.5
Bmedium positional1.260.5
Cmedium positional0.880.5
Dmedium positional0.990.5
Amedium thermal17.312
Bmedium thermal20.752
Cmedium thermal21.162
Dmedium thermal19.452
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 34 -
Rwork0.285 659 -
obs--80.02 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
146.598842.60340.0935
254.3826.703918.1895
361.371932.958110.4185
448.203940.549913.1926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A456 - 478
2X-RAY DIFFRACTION1A479 - 510
3X-RAY DIFFRACTION2D461 - 478
4X-RAY DIFFRACTION2D479 - 509
5X-RAY DIFFRACTION3B462 - 478
6X-RAY DIFFRACTION3B479 - 510
7X-RAY DIFFRACTION4C461 - 478
8X-RAY DIFFRACTION4C479 - 510

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