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- PDB-4kr1: Crystal structure of the kinetechore protein Iml3 from budding yeast -

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Basic information

Entry
Database: PDB / ID: 4kr1
TitleCrystal structure of the kinetechore protein Iml3 from budding yeast
ComponentsCentral kinetochore subunit IML3
KeywordsCELL CYCLE / chromosome segregation / kinetochore protein
Function / homology
Function and homology information


maintenance of meiotic sister chromatid cohesion / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / attachment of spindle microtubules to kinetochore / protein localization to chromosome, centromeric region / outer kinetochore / establishment of mitotic sister chromatid cohesion / kinetochore / cell division / nucleus
Similarity search - Function
Inner kinetochore subunit IML3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsTao, Y. / Guo, Q. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insights into the role of the Chl4-Iml3 complex in kinetochore assembly
Authors: Guo, Q. / Tao, Y. / Liu, H. / Teng, M. / Li, X.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Central kinetochore subunit IML3


Theoretical massNumber of molelcules
Total (without water)28,6591
Polymers28,6591
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.026, 73.026, 188.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Central kinetochore subunit IML3 / Increased minichromosome loss protein 3 / Minichromosome maintenance protein 19


Mass: 28659.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: IML3, MCM19, YBR107C, YBR0836 / Production host: Escherichia coli (E. coli) / References: UniProt: P38265
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3M Sodium formate, 100mM Cesium chloride, 3% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11039 / % possible obs: 99.9 % / Redundancy: 20.2 % / Biso Wilson estimate: 50.66 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 35.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 20.6 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.21 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.975 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.414 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 525 4.8 %RANDOM
Rwork0.2369 10430 --
obs0.238 10955 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 145.54 Å2 / Biso mean: 49.0334 Å2 / Biso min: 25.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 22 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221710
X-RAY DIFFRACTIONr_bond_other_d0.0010.021112
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.962321
X-RAY DIFFRACTIONr_angle_other_deg0.80232732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65524.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74315286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.755155
X-RAY DIFFRACTIONr_chiral_restr0.0530.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
X-RAY DIFFRACTIONr_mcbond_it0.8551.51089
X-RAY DIFFRACTIONr_mcbond_other0.0681.5438
X-RAY DIFFRACTIONr_mcangle_it1.621757
X-RAY DIFFRACTIONr_scbond_it5.2343621
X-RAY DIFFRACTIONr_scangle_it4.8294.5564
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 37 -
Rwork0.316 725 -
all-762 -
obs--99.22 %
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)
10.0592-0.08770.07451.0190.28372.67530.02370.0459-0.06470.0439-0.02080.1354-0.04890.3479-0.0030.05980.01530.00680.2165-0.03080.1007-16.8273-28.4523-23.7355
21.0637-0.31441.09490.1331-0.17311.7111-0.0005-0.0729-0.00420.00990.05220.00050.01180.0348-0.05180.0383-0.04850.01460.1375-0.0150.1703-23.8058-22.7415-20.9228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 243
2X-RAY DIFFRACTION2A301 - 322

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