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- PDB-4it3: Crystal Structure of Iml3 from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4it3
TitleCrystal Structure of Iml3 from S. cerevisiae
ComponentsCentral kinetochore subunit IML3
KeywordsCELL CYCLE / beta sheet / kinetochore / chl4 / nucleus
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 / outer kinetochore / protein localization to chromosome, centromeric region / 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: 2.495 Å
AuthorsHinshaw, S.M. / Harrison, S.C.
CitationJournal: Cell Rep / Year: 2013
Title: An iml3-chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation.
Authors: Hinshaw, S.M. / Harrison, S.C.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Central kinetochore subunit IML3


Theoretical massNumber of molelcules
Total (without water)28,7881
Polymers28,7881
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.135, 73.135, 189.133
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 28787.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IML3, MCM19, YBR107C, YBR0836 / Production host: Escherichia coli (E. coli) / References: UniProt: P38265
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.75 M sodium formate, 4% 2,5-diaminopentane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2012
RadiationMonochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.494→37.889 Å / Num. obs: 11048 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.103 / Χ2: 2.331 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.494-2.5413.50.8765250.924199.4
2.54-2.5913.80.7415320.924199.6
2.59-2.6413.50.6585450.961199.6
2.64-2.6913.60.5895220.977199.8
2.69-2.7513.80.4615431.054199.6
2.75-2.8213.50.3995471.1451100
2.82-2.8913.70.2965291.317199.8
2.89-2.9613.90.2865301.4281100
2.96-3.0513.40.2295531.553199.8
3.05-3.1513.80.2035411.7491100
3.15-3.2613.50.175372.046199.8
3.26-3.3913.30.145472.4871100
3.39-3.5513.20.1185402.973199.8
3.55-3.7312.80.1015683.321100
3.73-3.9712.70.0955483.671199.6
3.97-4.27120.0825624.183199.3
4.27-4.711.40.0725644.577199.5
4.7-5.3810.90.0715734.57199.7
5.38-6.7810.70.0745904.061199
6.78-37.8899.20.0616524.331196.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.495→37.889 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8157 / SU ML: 0.32 / σ(F): 0.91 / Phase error: 23.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1104 9.99 %10 PERCENT IN EACH SHELL
Rwork0.2237 ---
obs0.2269 11048 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.7 Å2 / Biso mean: 53.6006 Å2 / Biso min: 20.67 Å2
Refinement stepCycle: LAST / Resolution: 2.495→37.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 32 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041824
X-RAY DIFFRACTIONf_angle_d0.8082467
X-RAY DIFFRACTIONf_chiral_restr0.064280
X-RAY DIFFRACTIONf_plane_restr0.003307
X-RAY DIFFRACTIONf_dihedral_angle_d15.092684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.495-2.60840.31991280.26941160128895
2.6084-2.74580.28091350.269512121347100
2.7458-2.91780.25041340.238412151349100
2.9178-3.1430.29961350.249812171352100
3.143-3.45910.29961390.226112391378100
3.4591-3.95920.21031380.211512491387100
3.9592-4.98640.21791420.169312771419100
4.9864-37.89380.25651530.23691375152898
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)
12.2639-0.71140.5794.46130.27852.2446-0.03030.355-0.1682-0.42770.15660.05470.48210.1483-0.1030.34740.1009-0.00430.516-0.02750.30620.57924.697260.5074
29.4045-0.85512.10094.7503-5.15495.83270.4177-0.1272-1.241-1.0114-0.07852.32260.631-0.7042-0.38020.4345-0.0279-0.0280.6237-0.0170.484311.634722.743356.7618
36.79130.37850.10842.4746-3.34344.5739-0.1569-0.82370.44380.3846-0.01360.1141-0.7151-0.25620.39890.2450.1499-0.06770.38190.06740.300111.030345.130562.4576
43.9277-0.1627-0.55197.43022.20933.9233-0.10990.1678-0.3185-0.07370.10890.22160.39720.33870.01010.26570.1057-0.02390.4904-0.06870.2822.772827.618560.3012
55.5059-0.9997-2.83939.0485-1.50643.54470.24770.03540.22510.0089-0.0711-0.6154-0.4781.3659-0.3310.2296-0.0409-0.02430.5638-0.01510.276926.309740.832575.415
64.6137-0.63415.09531.1005-2.24897.9308-0.1584-0.2360.04790.2690.07240.0878-0.4577-0.01440.07020.2960.03360.04270.3563-0.05060.285315.27541.344983.0196
75.29833.6271-2.58784.0063-0.77932.60790.8684-0.44892.14440.69740.0880.261-0.2988-0.2353-1.04161.77180.41410.23880.9052-0.21381.068910.193552.183584.0417
86.21122.74993.94936.58954.4996.91890.1050.03830.0510.6042-0.0751-0.0351-1.24410.4111-0.05530.7786-0.10030.01250.4584-0.0360.424920.026750.379685.511
97.1189-0.84380.06273.07550.62795.27520.1013-0.34780.55230.17840.0386-0.5666-0.83140.9417-0.32680.3579-0.1167-0.04630.6124-0.01080.278425.829940.684584.6094
106.19190.3438-3.16493.0479-1.02413.338-0.1863-0.1303-0.29890.05080.1411-0.1330.32960.61520.07540.24430.03170.01290.394-0.05830.252220.418234.931471.7326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 0:27A0 - 27
2X-RAY DIFFRACTION2chain A and resid 28:37A28 - 37
3X-RAY DIFFRACTION3chain A and resid 38:52A38 - 52
4X-RAY DIFFRACTION4chain A and resid 53:114A53 - 114
5X-RAY DIFFRACTION5chain A and resid 115:125A115 - 125
6X-RAY DIFFRACTION6chain A and resid 126:170A126 - 170
7X-RAY DIFFRACTION7chain A and resid 171:179A171 - 179
8X-RAY DIFFRACTION8chain A and resid 180:199A180 - 199
9X-RAY DIFFRACTION9chain A and resid 200:212A200 - 212
10X-RAY DIFFRACTION10chain A and resid 213:242A213 - 242

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