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- PDB-2vpv: Dimerization Domain of Mif2p -

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Basic information

Entry
Database: PDB / ID: 2vpv
TitleDimerization Domain of Mif2p
ComponentsPROTEIN MIF2
KeywordsCELL CYCLE / NUCLEUS / MITOSIS / CENTROMERE / DNA-BINDING / KINETOCHORE / CELL DIVISION / PHOSPHOPROTEIN / JELLY-ROLL FOLD / DIMERIZATION DOMAIN
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / localization / mitotic spindle organization / chromosome segregation / kinetochore / cell division ...spindle attachment to meiosis I kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / localization / mitotic spindle organization / chromosome segregation / kinetochore / cell division / protein-containing complex binding / nucleus
Similarity search - Function
Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inner kinetochore subunit MIF2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsCohen, R.L. / Espelin, C.W. / Sorger, P.K. / Harrison, S.C. / Simons, K.T.
CitationJournal: Mol.Biol.Cell / Year: 2008
Title: Structural and Functional Dissection of Mif2P, a Conserved DNA-Binding Kinetochore Protein.
Authors: Cohen, R.L. / Espelin, C.W. / De Wulf, P. / Sorger, P.K. / Harrison, S.C. / Simons, K.T.
History
DepositionMar 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN MIF2
B: PROTEIN MIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5383
Polymers37,4422
Non-polymers961
Water48627
1
A: PROTEIN MIF2
B: PROTEIN MIF2
hetero molecules

A: PROTEIN MIF2
B: PROTEIN MIF2
hetero molecules

A: PROTEIN MIF2
B: PROTEIN MIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6159
Polymers112,3266
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12540 Å2
ΔGint-76 kcal/mol
Surface area31250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)106.020, 106.020, 106.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1531-

SO4

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9065, -0.3388, 0.252), (-0.3388, 0.2274, -0.913), (0.252, -0.913, -0.3209)
Vector: 140.3945, 142.5386, 139.5289)

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Components

#1: Protein PROTEIN MIF2 / MIF2P


Mass: 18721.082 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 365-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON-PLUS / References: UniProt: P35201
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 52.6 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR FUSION FROM 3-4% (W/V) PEG 3000, 100 MM IMIDAZOLE (PH 8.0), AND 70-100 MM LI2SO4 OR NA2SO4

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.5003
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5003 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 15323 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.5 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.74 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 468 4.8 %RANDOM
Rwork0.208 ---
obs0.21 9197 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 5 27 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9432003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8595177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7124.24266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.212154
X-RAY DIFFRACTIONr_chiral_restr0.1020.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021092
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9661.5899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81721456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9263591
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2234.5547
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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)
11.97221.1816-1.75012.9568-1.09272.80470.0677-0.2289-0.02890.2031-0.13370.0577-0.11760.24290.0661-0.0231-0.0623-0.0475-0.02390.0341-0.034971.132159.17290.4789
22.9495-1.0155-0.69543.11310.30873.8479-0.09360.0325-0.33820.29710.25780.60040.1081-0.5139-0.1642-0.09290.01170.02660.0640.05350.091149.593474.67578.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 530
2X-RAY DIFFRACTION2B439 - 530

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