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- PDB-6ah6: M500V mutant of Coronin coiled coil domain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ah6
TitleM500V mutant of Coronin coiled coil domain
ComponentsCoronin-like protein
KeywordsSTRUCTURAL PROTEIN / Clash mutant(M500V) of Coronin Coiled Coil domain
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: 2.5 Å
AuthorsAnsari, A. / Karade, S.S. / 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 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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
B: Coronin-like protein
C: Coronin-like protein
D: Coronin-like protein


Theoretical massNumber of molelcules
Total (without water)25,3494
Polymers25,3494
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-68 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.700, 49.830, 45.330
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Coronin-like protein


Mass: 6337.237 Da / Num. of mol.: 4 / Mutation: M500V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Cell: Flagellar protein / Plasmid: pET-28a / Details (production host): T7-promoter, His tagg / Production host: Escherichia coli (E. coli) / Variant (production host): Rossetta pLysS / References: UniProt: Q3T1U8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.37 Å3/Da / Density % sol: 48.08 % / Description: shovel blade shaped
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Lithium sulfate, ammonium sulphate, 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: 0.9795 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→18.12 Å / Num. obs: 8088 / % possible obs: 94.67 % / Redundancy: 2 % / Biso Wilson estimate: 49.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02494 / Rrim(I) all: 0.03527 / Net I/σ(I): 18.29
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.06221 / Mean I/σ(I) obs: 9.16 / Num. unique obs: 834 / CC1/2: 0.99 / Rrim(I) all: 0.08798 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CX2

5cx2


Resolution: 2.5→18.12 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2987 394 4.87 %5%
Rwork0.27 ---
obs-8082 95.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 0 28 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121393
X-RAY DIFFRACTIONf_angle_d1.3411886
X-RAY DIFFRACTIONf_dihedral_angle_d20.449495
X-RAY DIFFRACTIONf_chiral_restr0.09240
X-RAY DIFFRACTIONf_plane_restr0.007251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.5890.41171260.3262538X-RAY DIFFRACTION95
2.8606-3.59940.341220.30782586X-RAY DIFFRACTION96
3.5994-18.120.25481460.23132566X-RAY DIFFRACTION94
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)
17.9576-4.73552.24877.2353-0.41162.33250.5608-0.1799-0.1992-1.0976-0.12750.0830.1471-0.6984-0.37920.33090.00390.17430.4610.07460.308650.990838.13461.9957
23.3693-4.9062.76597.0798-3.33173.7559-0.07-0.38690.4614-0.00250.08-0.464-0.5588-0.2068-0.03410.40.04250.06870.4093-0.01760.351161.778734.96198.6598
34.665-3.93490.33934.699-0.98070.0626-0.1448-0.63140.58160.91280.246-0.4459-0.6324-0.8556-0.04520.70390.43950.34061.36830.00740.354652.939238.564215.4401
43.4536-0.57011.15960.9038-0.11760.28930.152-1.2551-1.020.2710.38010.3421-0.1328-0.8266-0.41530.58440.10930.20531.30940.38350.576455.931726.259117.5018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 462 through 509 )
2X-RAY DIFFRACTION2chain 'B' and (resid 469 through 508 )
3X-RAY DIFFRACTION3chain 'C' and (resid 466 through 509 )
4X-RAY DIFFRACTION4chain 'D' and (resid 462 through 510 )

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