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- PDB-6zpm: Crystal structure of the unconventional kinetochore protein Trypa... -

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Basic information

Entry
Database: PDB / ID: 6zpm
TitleCrystal structure of the unconventional kinetochore protein Trypanosoma cruzi KKT4 coiled coil domain
ComponentsTrypanosoma cruzi KKT4 117-218
KeywordsCELL CYCLE / KKT4 / kinetochore / kinetoplastids / microtubules
Function / homologyBRCT domain superfamily / THREONINE / Putative kinetoplastid kinetochore protein 4
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsLudzia, P. / Lowe, D.E. / 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y ..._pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.selection_details
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

Downloads & links

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Assembly

Deposited unit
A: Trypanosoma cruzi KKT4 117-218
B: Trypanosoma cruzi KKT4 117-218
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9933
Polymers24,8742
Non-polymers1191
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-54 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.620, 25.310, 136.880
Angle α, β, γ (deg.)90.000, 96.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 116 through 191 or resid 193...
21(chain B and ((resid 0 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 116 through 191 or resid 193...A116 - 191
121(chain A and (resid 116 through 191 or resid 193...A193
131(chain A and (resid 116 through 191 or resid 193...A195 - 205
141(chain A and (resid 116 through 191 or resid 193...A207 - 215
211(chain B and ((resid 0 and (name N or name...B0
221(chain B and ((resid 0 and (name N or name...B116 - 215
231(chain B and ((resid 0 and (name N or name...B116 - 215
241(chain B and ((resid 0 and (name N or name...B116 - 215
251(chain B and ((resid 0 and (name N or name...B116 - 215

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Components

#1: Protein Trypanosoma cruzi KKT4 117-218


Mass: 12437.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residue Gly is not visible in the electron density.
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_122g72 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2WCI2
#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: HEPES, sodium chloride, MOPSO, Bis-Tris, DL-Arginine hydrochloride, DL- Threonine, DL-Histidine monohydrochloride monohydrate, DL-5-Hydroxylysine hydrochloride, trans-4-hydroxy-L-proline, ...Details: HEPES, sodium chloride, MOPSO, Bis-Tris, DL-Arginine hydrochloride, DL- Threonine, DL-Histidine monohydrochloride monohydrate, DL-5-Hydroxylysine hydrochloride, trans-4-hydroxy-L-proline, PEG 8000, 1,5- Pentanediol, TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→67.96 Å / Num. obs: 16787 / % possible obs: 90.36 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→3.88 Å / Num. unique obs: 1452 / CC1/2: 0.274

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
Arcimboldophasing
BUCCANEERmodel building
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→67.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1678 10 %
Rwork0.2412 15109 -
obs0.2429 16787 90.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.44 Å2 / Biso mean: 37.1107 Å2 / Biso min: 8.96 Å2
Refinement stepCycle: final / Resolution: 1.9→67.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 17 184 1841
Biso mean--54.85 37.97 -
Num. residues----203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A797X-RAY DIFFRACTION13.226TORSIONAL
12B797X-RAY DIFFRACTION13.226TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.960.4675270.337523326017
1.96-2.020.321010.2923915101668
2.02-2.090.28061550.280114171572100
2.09-2.180.24471500.244313361486100
2.18-2.280.24791520.232113691521100
2.28-2.40.27291570.240813821539100
2.4-2.550.25341540.252213971551100
2.55-2.740.26011550.251413911546100
2.74-3.020.25271530.247613861539100
3.02-3.460.2281560.222314011557100
3.46-4.350.2351500.219514351585100
4.36-67.960.29121680.25151447161598
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)
10.2041-0.15071.3715-0.9235-0.72736.1384-0.21660.02960.07230.21950.0093-0.1026-0.830.14210.18210.96310.0417-0.20020.2597-0.04350.200723.46512.013118.941
20.30740.35021.4053-0.68041.15647.54210.1624-0.0182-0.00970.24660.0634-0.09650.6576-0.064-0.21420.76280.1352-0.07560.19120.00290.186224.5717.347123.456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 116:218 )A116 - 218
2X-RAY DIFFRACTION2( CHAIN B AND RESID 116:215 )B116 - 215

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