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- PDB-5j6p: Crystal Structure of Mis18(17-118) from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 5j6p
TitleCrystal Structure of Mis18(17-118) from Schizosaccharomyces pombe
ComponentsKinetochore protein mis18
KeywordsCELL CYCLE / Mis18 / centromere assembly
Function / homology
Function and homology information


CENP-A recruiting complex / CENP-A containing chromatin assembly / chromosome, centromeric region / chromosome segregation / kinetochore / cell division / chromatin / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Mis18 domain / Mis18 domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
Similarity search - Domain/homology
Kinetochore protein mis18
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWang, C. / Shao, C. / Zhang, M. / Zhang, X. / Zang, J.
CitationJournal: To Be Published
Title: Crystal Structure of Mis18(17-118) from Schizosaccharomyces pombe
Authors: Shao, C. / Wang, C. / Zhang, M. / Zhang, X. / Zang, J.
History
DepositionApr 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Derived calculations / Category: struct_site / struct_site_gen
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Kinetochore protein mis18
A: Kinetochore protein mis18
C: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5856
Polymers38,3893
Non-polymers1963
Water543
1
B: Kinetochore protein mis18
A: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7234
Polymers25,5922
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area11500 Å2
MethodPISA
2
C: Kinetochore protein mis18
hetero molecules

C: Kinetochore protein mis18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7234
Polymers25,5922
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,x-y-1,-z-11
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.568, 120.568, 73.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Kinetochore protein mis18


Mass: 12796.233 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 18-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mis18, SPCC970.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P802
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.17 Å3/Da / Density % sol: 70.51 % / Description: rhombus
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M (NH4)2SO4, 20% PEG 3350, 0.4M 1,6-Hexanediol, 0.1M Tris pH 8.5, 4% Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→60.39 Å / Num. obs: 18911 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata processing
SCALAdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→46.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.89 / SU B: 14.024 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29436 971 5.1 %RANDOM
Rwork0.22518 ---
obs0.22849 17884 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.122 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å21.6 Å20 Å2
2--3.21 Å2-0 Å2
3----10.41 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 3 3 2431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022470
X-RAY DIFFRACTIONr_bond_other_d0.0030.022243
X-RAY DIFFRACTIONr_angle_refined_deg2.021.9453338
X-RAY DIFFRACTIONr_angle_other_deg1.1735170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.585299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49524.524126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.2615429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5751515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02588
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4798.2791205
X-RAY DIFFRACTIONr_mcbond_other6.4718.2761204
X-RAY DIFFRACTIONr_mcangle_it9.14912.4081501
X-RAY DIFFRACTIONr_mcangle_other9.14612.4111502
X-RAY DIFFRACTIONr_scbond_it6.9298.8551265
X-RAY DIFFRACTIONr_scbond_other6.9278.8561266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.99113.0631838
X-RAY DIFFRACTIONr_long_range_B_refined12.07165.6972682
X-RAY DIFFRACTIONr_long_range_B_other12.06965.7132683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 72 -
Rwork0.45 1287 -
obs--96.86 %

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