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- PDB-5m97: Structure of the Mal3 EB1-like domain -

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Basic information

Entry
Database: PDB / ID: 5m97
TitleStructure of the Mal3 EB1-like domain
ComponentsMicrotubule integrity protein mal3
KeywordsCELL CYCLE / EB1 domain / microtubule-binding / coiled-coil
Function / homology
Function and homology information


dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / nuclear migration involved in conjugation with cellular fusion / cell cortex of cell tip / cortical microtubule / mitotic spindle astral microtubule / karyogamy involved in conjugation with cellular fusion / mitotic spindle pole body / nuclear microtubule / mitotic spindle midzone ...dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / nuclear migration involved in conjugation with cellular fusion / cell cortex of cell tip / cortical microtubule / mitotic spindle astral microtubule / karyogamy involved in conjugation with cellular fusion / mitotic spindle pole body / nuclear microtubule / mitotic spindle midzone / astral microtubule / protein localization to microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule organizing center / microtubule lateral binding / ATPase activator activity / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / molecular condensate scaffold activity / microtubule cytoskeleton / microtubule binding / cell division / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule integrity protein mal3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.33 Å
AuthorsZakian, S. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
CitationJournal: J. Cell. Sci. / Year: 2016
Title: An unconventional interaction between Dis1/TOG and Mal3/EB1 in fission yeast promotes the fidelity of chromosome segregation.
Authors: Matsuo, Y. / Maurer, S.P. / Yukawa, M. / Zakian, S. / Singleton, M.R. / Surrey, T. / Toda, T.
History
DepositionOct 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Microtubule integrity protein mal3
A: Microtubule integrity protein mal3


Theoretical massNumber of molelcules
Total (without water)18,0602
Polymers18,0602
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-36 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 37.910, 101.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Microtubule integrity protein mal3


Mass: 9030.100 Da / Num. of mol.: 2 / Fragment: UNP residues 174-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mal3, SPAC18G6.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10113
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.1 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 30% MPD and 0.1 M sodium acetate at pH4.6

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.33→35.52 Å / Num. obs: 32150 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.0925 / Net I/σ(I): 16.19
Reflection shellResolution: 1.33→1.378 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.963 / Mean I/σ(I) obs: 1.15 / CC1/2: 0.571 / % possible all: 99

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.33→35.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1570 4.9 %RANDOM
Rwork0.1942 ---
obs0.195 32150 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.92 Å2 / Biso mean: 22.3733 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--1.72 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.33→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 0 114 1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0191159
X-RAY DIFFRACTIONr_bond_other_d00.021106
X-RAY DIFFRACTIONr_angle_refined_deg2.5191.9641564
X-RAY DIFFRACTIONr_angle_other_deg3.69832542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4395138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.412564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77115233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.868159
X-RAY DIFFRACTIONr_chiral_restr0.1580.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021319
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02274
X-RAY DIFFRACTIONr_mcbond_it2.7181.604546
X-RAY DIFFRACTIONr_mcbond_other2.5711.595545
X-RAY DIFFRACTIONr_mcangle_it3.8692.388686
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 121 -
Rwork0.342 2197 -
all-2318 -
obs--98.55 %

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