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- PDB-6zpj: Crystal structure of the unconventional kinetochore protein Leish... -

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Basic information

Entry
Database: PDB / ID: 6zpj
TitleCrystal structure of the unconventional kinetochore protein Leishmania mexicana KKT4 coiled coil domain
ComponentsLeishmania mexicana KKT4
KeywordsCELL CYCLE / kinetochore / kinetoplastid / microtubules / coiled coil
Function / homologySMC5-SMC6 complex localization factor protein 1 / protein localization to site of double-strand break / positive regulation of double-strand break repair / BRCT domain superfamily / site of double-strand break / DNA damage response / nucleus / IMIDAZOLE / BRCT domain-containing protein
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsLudzia, P. / Lowe, E.D. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
Citation
Journal: Structure / Year: 2021
Title: Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein.
Authors: Ludzia, P. / Lowe, E.D. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
#1: Journal: Biorxiv / Year: 2020
Title: Structural characterisation of KKT4, an unconventional microtubule-binding kinetochore protein
Authors: Ludzia, P. / Lowe, E. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leishmania mexicana KKT4
B: Leishmania mexicana KKT4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2076
Polymers28,8332
Non-polymers3754
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-43 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.310, 37.710, 122.390
Angle α, β, γ (deg.)90.000, 92.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Leishmania mexicana KKT4 / Leishmania mexicana KKT4


Mass: 14416.385 Da / Num. of mol.: 2 / Mutation: R218Q
Source method: isolated from a genetically manipulated source
Details: Expressed protein contains an additional 23 residues from the expression vector at its C-terminus due to a cloning error, which failed to place a stop codon after the KKT4 coding sequence. ...Details: Expressed protein contains an additional 23 residues from the expression vector at its C-terminus due to a cloning error, which failed to place a stop codon after the KKT4 coding sequence. Only 7 out of 23 residues were visible in the electron density.
Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote)
Gene: LMXM_10_0300 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9AN40
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, sodium chloride, imidazole, MPD, TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.9→61.1511 Å / Num. obs: 22522 / % possible obs: 98.34 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.1
Reflection shellResolution: 1.9→4.322 Å / Num. unique obs: 1840 / CC1/2: 0.352 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Arcimboldophasing
BUCCANEERmodel building
Aimlessdata scaling
DIALSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→61.15 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.9208 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2318 1068 4.75 %
Rwork0.1986 21434 -
obs0.2001 22502 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 26 264 1738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01481527
X-RAY DIFFRACTIONf_angle_d1.33342063
X-RAY DIFFRACTIONf_chiral_restr0.0787236
X-RAY DIFFRACTIONf_plane_restr0.0088280
X-RAY DIFFRACTIONf_dihedral_angle_d22.5417578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.26351250.24612645X-RAY DIFFRACTION97.54
1.99-2.090.26851220.22452667X-RAY DIFFRACTION97.62
2.09-2.220.24131430.19372634X-RAY DIFFRACTION98.16
2.22-2.390.23221470.17692612X-RAY DIFFRACTION98.25
2.39-2.630.24981380.19012677X-RAY DIFFRACTION98.77
2.63-3.020.23871260.19612687X-RAY DIFFRACTION98.84
3.02-3.80.20121480.17212723X-RAY DIFFRACTION99.17
3.8-61.150.22631190.2182789X-RAY DIFFRACTION98.38
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)
10.0107030025328-0.0111306209703-0.00705608324433-0.01315124239910.001437865924420.107361618530.00615610572685-0.4587655709680.04418191835160.02883358574350.0157392781183-0.0239893962241-0.02552091222170.1970984746670.06086822993570.164189540033-0.00243941395795-0.04071734719470.3433407808410.05703661803460.16731756068456.6461692408-6.5761949392391.3738741953
23.79574166308-0.408993563523.052122837190.220310642269-0.3222591588543.177037116160.182345056031-0.212187218854-0.223094212680.0190719522714-0.0253903680703-0.01632593594190.1365576976080.119666480296-0.156835467910.141950618885-0.02357169706420.003120964685690.1315917451260.03352147491060.10589832460137.7227072635-8.5631101468578.1321948287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 291 )
2X-RAY DIFFRACTION2chain 'B' and (resid 182 through 258 )

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