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- PDB-3n4r: Structure of Csm1 C-terminal domain, R3 form -

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Basic information

Entry
Database: PDB / ID: 3n4r
TitleStructure of Csm1 C-terminal domain, R3 form
ComponentsMonopolin complex subunit CSM1
KeywordsREPLICATION / meiosis / rDNA
Function / homology
Function and homology information


monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / nuclear envelope / nucleolus / identical protein binding
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Monopolin complex subunit CSM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.602 Å
AuthorsCorbett, K.D. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The Monopolin Complex Crosslinks Kinetochore Components to Regulate Chromosome-Microtubule Attachments.
Authors: Corbett, K.D. / Yip, C.K. / Ee, L.S. / Walz, T. / Amon, A. / Harrison, S.C.
History
DepositionMay 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
C: Monopolin complex subunit CSM1
D: Monopolin complex subunit CSM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,76111
Polymers53,5024
Non-polymers1,2597
Water1,42379
1
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4326
Polymers26,7512
Non-polymers6814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-23 kcal/mol
Surface area10150 Å2
MethodPISA
2
C: Monopolin complex subunit CSM1
D: Monopolin complex subunit CSM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3305
Polymers26,7512
Non-polymers5793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 72.470, 267.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Monopolin complex subunit CSM1 / / Chromosome segregation in meiosis protein 1


Mass: 13375.534 Da / Num. of mol.: 4 / Fragment: C-terminal domain (residues 69-181) / Mutation: L157M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CSM1, SPO86, YCR086W, YCR86W / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P25651
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4
Details: 2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97182 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2008 / Details: mirrors
RadiationMonochromator: cryogenically-cooled 220 silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97182 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 16079 / Num. obs: 16079 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 66.1 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 3218 / Rsym value: 0.553 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.602→45.755 Å / SU ML: 1.18 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 805 5.01 %random
Rwork0.2211 ---
obs0.2222 16063 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.235 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2981 Å2-0 Å2-0 Å2
2--8.2981 Å20 Å2
3----19.464 Å2
Refinement stepCycle: LAST / Resolution: 2.602→45.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 85 79 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033195
X-RAY DIFFRACTIONf_angle_d0.6834284
X-RAY DIFFRACTIONf_dihedral_angle_d16.9171139
X-RAY DIFFRACTIONf_chiral_restr0.047471
X-RAY DIFFRACTIONf_plane_restr0.002527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.602-2.76460.34111330.29992525X-RAY DIFFRACTION100
2.7646-2.9780.33671460.27182541X-RAY DIFFRACTION100
2.978-3.27770.31721240.25932567X-RAY DIFFRACTION100
3.2777-3.75180.23631250.2252537X-RAY DIFFRACTION100
3.7518-4.72610.23881530.18252537X-RAY DIFFRACTION100
4.7261-45.76210.19571240.21242551X-RAY DIFFRACTION100
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)
11.9097-1.3623-1.59721.82470.59393.32550.47980.37720.0023-0.1261-0.6832-0.39740.1054-0.08290.00020.4923-0.02260.01670.95530.15340.656919.6084-26.045-30.0471
23.0390.2169-0.0313.5889-0.41751.68480.13340.17810.1533-0.2327-0.1895-0.0109-0.37440.373-0.00050.4942-0.07340.03960.48940.00980.552911.7819-24.9783-9.1035
35.27930.57991.53033.2603-0.52714.50010.06670.3477-0.3423-0.28840.1311-0.0050.4064-0.018800.6792-0.0289-0.07760.5358-0.07490.607712.1582-24.147215.2695
40.6132-0.9706-1.57271.97120.82913.9353-0.120.11590.1980.76080.1005-0.3721-0.1609-0.23550.00020.7739-0.0269-0.10260.4617-0.03920.554615.1719-14.420733.5261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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