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- PDB-6adz: LdCoroCC Double mutant- I486A-L493A -

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Basic information

Entry
Database: PDB / ID: 6adz
TitleLdCoroCC Double mutant- I486A-L493A
ComponentsCoronin-like protein
KeywordsSTRUCTURAL PROTEIN / Coiled coil domain of Actin interacting protein Coronin from Leishmania
Function / homology
Function and homology information


actin filament organization / actin filament binding / ribosome / ribonucleoprotein complex
Similarity search - Function
DUF1900 / Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...DUF1900 / Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 2.431 Å
AuthorsKarade, S.S. / Ansari, A. / Pratap, J.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
Citation
Journal: Int.J.Biol.Macromol. / Year: 2020
Title: Molecular and structural analysis of a mechanical transition of helices in the L. donovani coronin coiled-coil domain.
Authors: Karade, S.S. / Ansari, A. / Srivastava, V.K. / Nayak, A.R. / Pratap, J.V.
#1: Journal: 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. / Pratap, J.V.
History
DepositionAug 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coronin-like protein
C: Coronin-like protein
B: Coronin-like protein
D: Coronin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3336
Polymers25,1414
Non-polymers1922
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-90 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.877, 67.877, 208.381
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Coronin-like protein / Coronin (Coiled coil domain) double mutant


Mass: 6285.142 Da / Num. of mol.: 4 / Mutation: I486A, L493A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Cell: flagellar / Plasmid: pET-28a / Details (production host): T-7 promoter, His tagg / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q3T1U8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.76 Å3/Da / Density % sol: 55.37 % / Description: Hexagonal shaped
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 5.6
Details: Lithium sulfate, Ammonium sulfate and Sodium citrate 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.43→26.32 Å / Num. obs: 11408 / % possible obs: 99.7 % / Redundancy: 16.1 % / Biso Wilson estimate: 62.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0591 / Rrim(I) all: 0.061 / Net I/σ(I): 24.96
Reflection shellResolution: 2.43→2.517 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 1056 / CC1/2: 0.903 / % possible all: 96.91

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000V703gdata reduction
HKL-2000V703gdata scaling
PHASER1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ADO

6ado


Resolution: 2.431→26.316 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.28
RfactorNum. reflection% reflectionSelection details
Rfree0.3143 1075 10.22 %5%
Rwork0.2767 ---
obs0.2807 10520 92.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.431→26.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 10 11 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061422
X-RAY DIFFRACTIONf_angle_d0.9761913
X-RAY DIFFRACTIONf_dihedral_angle_d17.635519
X-RAY DIFFRACTIONf_chiral_restr0.06226
X-RAY DIFFRACTIONf_plane_restr0.015259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4308-2.54140.44791120.3975915X-RAY DIFFRACTION76
2.5414-2.67520.38191230.39131045X-RAY DIFFRACTION84
2.6752-2.84270.40071290.35481105X-RAY DIFFRACTION89
2.8427-3.06190.41441340.35191168X-RAY DIFFRACTION94
3.0619-3.36940.38381340.32661235X-RAY DIFFRACTION97
3.3694-3.85570.27991390.25461252X-RAY DIFFRACTION98
3.8557-4.85280.32991470.27021311X-RAY DIFFRACTION99
4.8528-26.3180.26561570.24071414X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14731.4512-0.63932.297-0.84550.3389-0.37040.7130.5949-0.02240.70021.01170.1791-0.42120.2130.8914-0.188-0.01440.5574-0.04360.538630.75194.4315109.8195
21.9823-3.9449-0.87349.51633.52082.55610.7732-0.1316-0.725-1.3593-0.71630.6828-0.2742-1.4157-0.01080.4368-0.04080.12740.71590.19090.577816.316835.5281116.6066
30.2849-0.320.22570.8702-0.90060.89480.04070.0003-0.1611-0.43120.24-0.49030.98970.58880.241.0453-0.02840.2790.747-0.0080.687532.047924.5796102.874
40.2941-0.2225-0.25870.16410.19880.21910.5081-1.09461.4790.1281-0.2292-0.791-1.0288-0.1002-0.29650.80170.1080.16590.8652-0.43511.062924.184150.5224124.2424
5-0.05890.19130.3050.63330.65540.3446-0.3936-1.3961-0.0459-0.6031.29710.1968-0.52560.84310.8490.6609-0.02070.20970.87270.10740.556721.699937.5152122.266
60.17260.1222-0.06160.7917-0.01430.20870.02050.0669-0.1795-0.3684-0.0139-0.02640.12460.0650.39691.7846-0.46430.9160.41070.18061.154618.034658.1498119.7904
70.3148-0.1695-0.61451.52250.08880.6220.81310.1586-0.0546-1.003-0.82341.0948-0.7382-0.81620.00640.96380.06550.03160.65090.07160.710122.374427.3101105.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 463 through 481 )
2X-RAY DIFFRACTION2chain 'A' and (resid 482 through 510 )
3X-RAY DIFFRACTION3chain 'C' and (resid 462 through 495 )
4X-RAY DIFFRACTION4chain 'C' and (resid 496 through 509 )
5X-RAY DIFFRACTION5chain 'B' and (resid 460 through 510 )
6X-RAY DIFFRACTION6chain 'D' and (resid 464 through 474 )
7X-RAY DIFFRACTION7chain 'D' and (resid 475 through 509 )

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