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- PDB-3n4s: Structure of Csm1 C-terminal domain, P21212 form -

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Basic information

Entry
Database: PDB / ID: 3n4s
TitleStructure of Csm1 C-terminal domain, P21212 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
Monopolin complex subunit CSM1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,43814
Polymers53,0554
Non-polymers2,38310
Water2,972165
1
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2425
Polymers26,5272
Non-polymers7153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-30 kcal/mol
Surface area11460 Å2
MethodPISA
2
C: Monopolin complex subunit CSM1
D: Monopolin complex subunit CSM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1959
Polymers26,5272
Non-polymers1,6687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-28 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.975, 134.044, 54.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 13263.705 Da / Num. of mol.: 4 / Fragment: C-terminal domain (residues 69-181)
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.: 10 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0 M Sodium malonate pH 6.4, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 22014 / Num. obs: 22014 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 43.2 Å2 / Rsym value: 0.071 / Net I/σ(I): 25.7
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1039 / Rsym value: 0.497 / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N4R

3n4r


Resolution: 2.35→48.402 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1128 5.14 %random
Rwork0.2075 ---
obs0.2088 21942 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.39 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.4501 Å20 Å2-0 Å2
2--12.1077 Å20 Å2
3----1.6576 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 160 165 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053465
X-RAY DIFFRACTIONf_angle_d0.9494613
X-RAY DIFFRACTIONf_dihedral_angle_d22.5991308
X-RAY DIFFRACTIONf_chiral_restr0.064500
X-RAY DIFFRACTIONf_plane_restr0.004552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4570.31331410.27562487X-RAY DIFFRACTION97
2.457-2.58660.29631310.23882602X-RAY DIFFRACTION100
2.5866-2.74860.25671340.2332549X-RAY DIFFRACTION100
2.7486-2.96080.26771510.22112564X-RAY DIFFRACTION100
2.9608-3.25870.23591420.2132576X-RAY DIFFRACTION100
3.2587-3.73010.21441390.17692622X-RAY DIFFRACTION100
3.7301-4.69890.1771380.1632651X-RAY DIFFRACTION100
4.6989-48.41230.23511520.21922763X-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)
11.976-0.7028-0.41771.10930.2550.5718-0.15130.17420.0330.09550.1312-0.1371-0.082-0.000100.216-0.01740.07630.1942-0.02030.264522.2169-13.8471-29.8734
22.5188-0.421-0.48821.1725-0.66231.1086-0.03840.1442-0.1684-0.08150.07140.07090.0238-0.0692-00.1679-0.04210.04180.1057-0.04350.20932.7568-20.015-21.4896
30.8095-0.31121.59410.8635-0.29221.5205-0.10020.2092-0.02610.11950.00290.074-0.17120.335500.2177-0.0047-0.0590.3474-0.00060.169328.933513.91569.1859
41.4024-0.90181.57621.6245-0.74921.93380.0188-0.03220.0384-0.1246-0.0456-0.070.02410.2498-00.1932-0.0155-0.01140.16870.00210.136917.391911.0612-9.3186
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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