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- PDB-6icr: LdCoroCC mutant- C482A -

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Basic information

Entry
Database: PDB / ID: 6icr
TitleLdCoroCC mutant- C482A
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. ...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
Guanine nucleotide-binding protein subunit beta-like protein / Coronin
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsKarade, S.S. / Srivastava, V.K. / Ansari, A. / Pratap, J.V.
CitationJournal: 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.
History
DepositionSep 6, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 1.3Feb 12, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4797
Polymers25,2934
Non-polymers1863
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-66 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.480, 49.720, 45.730
Angle α, β, γ (deg.)90.00, 110.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Coronin-like protein


Mass: 6323.211 Da / Num. of mol.: 4 / Mutation: C482A, T509S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pET-28a / Details (production host): T7-promotor with his tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q3T1U8, UniProt: E9AWD4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.47 Å3/Da / Density % sol: 55.21 % / Description: Rectangular shaped
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Lithium sulfate 0.8M, ammonium sulfate 0.85M, sodium citrate buffer 0.1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.04→33.644 Å / Num. obs: 15839 / % possible obs: 99.62 % / Redundancy: 7.6 % / Biso Wilson estimate: 39.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04409 / Rrim(I) all: 0.04735 / Net I/av σ(I): 18.73 / Net I/σ(I): 16.16
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.0664 / Mean I/σ(I) obs: 12.44 / Num. unique obs: 1103 / CC1/2: 0.999 / Rrim(I) all: 0.0711 / % possible all: 99.82

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CX2

5cx2


Resolution: 2.04→33.644 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3053 794 5.01 %
Rwork0.2632 --
obs0.2654 15839 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→33.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 12 26 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041462
X-RAY DIFFRACTIONf_angle_d0.6651962
X-RAY DIFFRACTIONf_dihedral_angle_d15.735549
X-RAY DIFFRACTIONf_chiral_restr0.024239
X-RAY DIFFRACTIONf_plane_restr0.002260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.16780.37571330.312480X-RAY DIFFRACTION100
2.1678-2.33510.37411070.31162509X-RAY DIFFRACTION100
2.3351-2.570.38051310.29192502X-RAY DIFFRACTION100
2.57-2.94180.32461370.30812500X-RAY DIFFRACTION100
2.9418-3.70560.30741370.27352509X-RAY DIFFRACTION100
3.7056-33.64820.27071490.22622545X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.8403 Å / Origin y: -29.947 Å / Origin z: -32.5452 Å
111213212223313233
T0.2737 Å2-0.0046 Å20.0421 Å2-0.564 Å20.0233 Å2--0.3288 Å2
L6.4739 °2-3.0303 °21.9195 °2-3.5112 °2-0.7728 °2--1.4435 °2
S-0.4088 Å °-1.3459 Å °0.1194 Å °0.1933 Å °0.7128 Å °0.0872 Å °-0.0312 Å °-0.5393 Å °-0.2548 Å °
Refinement TLS groupSelection details: all

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