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- PDB-6ado: LdCoroCC mutant-I486A -

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Basic information

Entry
Database: PDB / ID: 6ado
TitleLdCoroCC mutant-I486A
ComponentsCoronin-like protein
KeywordsSTRUCTURAL PROTEIN / Mutant of actin-associated protein coronin of leishmania donovani
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: 2.502 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 1, 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 1.3Mar 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

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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


Theoretical massNumber of molelcules
Total (without water)25,3094
Polymers25,3094
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-72 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.338, 53.338, 142.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Coronin-like protein / I486A mutant of LdCoroCC


Mass: 6327.222 Da / Num. of mol.: 4 / Mutation: I486A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Cell: fragiler protein / Plasmid: pET-28a / Details (production host): expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / Variant (production host): pLysS / References: UniProt: Q3T1U8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: diamond shaped
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Lithium sulfate, Ammonium sulfate and Sodium citrate (pH 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: 2.502→21.98 Å / Num. obs: 8646 / % possible obs: 99.82 % / Redundancy: 5.4 % / Biso Wilson estimate: 53.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.068 / Net I/σ(I): 17.55
Reflection shellResolution: 2.502→2.591 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.83 / Num. unique obs: 827 / CC1/2: 0.979 / % possible all: 99.52

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000v703gdata reduction
HKL-2000v703gdata scaling
PHASERV1.8.4.1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→21.977 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2945 407 4.72 %5
Rwork0.2684 ---
obs0.2696 8615 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→21.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 14 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111450
X-RAY DIFFRACTIONf_angle_d1.1281950
X-RAY DIFFRACTIONf_dihedral_angle_d18.022537
X-RAY DIFFRACTIONf_chiral_restr0.075239
X-RAY DIFFRACTIONf_plane_restr0.004258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5019-2.86330.35611330.34852649X-RAY DIFFRACTION100
2.8633-3.60490.32071360.30532708X-RAY DIFFRACTION100
3.6049-21.9780.27071380.2372851X-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)
12.891-1.70380.65841.9003-0.41170.966-0.4168-0.3167-0.43710.36880.60310.8455-0.3813-1.1916-1.46170.44880.41580.00540.80940.05430.328711.61795.289968.9767
26.89222.3184-0.640.7865-0.40195.361-0.03440.20860.540.3161-0.4179-1.20960.35721.08351.13410.89360.3665-0.44161.10620.04661.49311.788738.660954.6763
33.8474-1.23970.57856.05061.12150.54290.81420.3753-0.7469-0.9963-0.69430.75610.4144-0.12150.0030.51440.0272-0.00390.6145-0.05390.516117.7045-12.376962.5194
41.2190.61011.19557.4455-0.12131.2455-0.1978-0.2336-0.01320.10230.2446-0.5062-0.07010.1536-0.050.65560.3843-0.01550.7439-0.10960.261117.405420.362857.4187
52.94380.96983.8668.2936-0.02035.4789-0.376-0.02390.43230.8011-0.20210.6249-1.4419-0.39960.53190.84930.20650.05950.9076-0.19260.557515.237444.396659.4172
60.776-0.6604-0.00983.9859-0.66840.1148-1.0694-0.79420.1750.7881.532-0.109-0.3258-0.2611-0.38140.67410.319-0.0670.8453-0.10810.394613.294123.886965.0256
71.00850.4412-0.73487.876-1.72221.8398-0.0917-0.03360.0564-0.91160.01790.081-0.00850.67510.17230.96950.2649-0.11850.939-0.0830.439510.814433.095651.1196
84.08131.3379-0.98543.8755-0.97281.8383-0.3667-0.1624-0.73470.71370.36650.4354-0.3619-0.77260.31580.54510.26940.24950.9380.19910.51649.0141.751160.6322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 463 through 505 )
2X-RAY DIFFRACTION2chain 'A' and (resid 506 through 510 )
3X-RAY DIFFRACTION3chain 'C' and (resid 459 through 478 )
4X-RAY DIFFRACTION4chain 'C' and (resid 479 through 503 )
5X-RAY DIFFRACTION5chain 'C' and (resid 504 through 510 )
6X-RAY DIFFRACTION6chain 'B' and (resid 462 through 510 )
7X-RAY DIFFRACTION7chain 'D' and (resid 460 through 489 )
8X-RAY DIFFRACTION8chain 'D' and (resid 490 through 504 )

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