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- PDB-2q6q: Crystal structure of Spc42p, a critical component of spindle pole... -

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Basic information

Entry
Database: PDB / ID: 2q6q
TitleCrystal structure of Spc42p, a critical component of spindle pole body in budding yeast
ComponentsSpindle pole body component SPC42
KeywordsCELL CYCLE / Spc42p / spindle pole body / budding yeast
Function / homology
Function and homology information


intermediate layer of spindle pole body / central plaque of spindle pole body / spindle pole body duplication / regulation of microtubule nucleation / structural constituent of cytoskeleton / nucleus / cytoplasm
Similarity search - Function
Spindle pole body component Spc42 / Spindle pole body component Spc42p / Geminin coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Spindle pole body component SPC42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMalashkevich, V.N. / Newman, J.R. / Kim, P.S.
CitationJournal: Biochemistry / Year: 2008
Title: Analysis of coiled-coil interactions between core proteins of the spindle pole body.
Authors: Zizlsperger, N. / Malashkevich, V.N. / Pillay, S. / Keating, A.E.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindle pole body component SPC42
B: Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9276
Polymers17,7142
Non-polymers2124
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-62.7 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.860, 57.790, 57.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spindle pole body component SPC42 /


Mass: 8857.232 Da / Num. of mol.: 2 / Fragment: residues 65-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPC42 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS / References: UniProt: P36094
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 100 mM Tris, 200 mM cobalt chloride, 25% PEG 3350, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2001 / Details: X4A
RadiationMonochromator: X4A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→35 Å / Num. all: 10537 / Num. obs: 9799 / % possible obs: 93.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.2
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.37 / % possible all: 47

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GCN4

Resolution: 1.97→18.36 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.876 / SU B: 9.951 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29655 475 4.8 %RANDOM
Rwork0.21163 ---
obs0.21565 9404 94.68 %-
all-10055 --
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: 36.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.97→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 4 119 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9082.0041428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56227.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53215260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.793154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.2503
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2751
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8421.5636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.27501030
X-RAY DIFFRACTIONr_scbond_it20.77850438
X-RAY DIFFRACTIONr_scangle_it7.6074.5397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 19 -
Rwork0.248 391 -
obs--55.18 %
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)
16.4641.62333.6420.55961.07872.2291-0.0553-0.1149-0.0938-0.05770.0426-0.0204-0.042-0.03980.01270.012-0.026-0.0129-0.03320.0251-0.03434.52888.39589.9544
25.2387-0.05522.67090.08310.01581.46210.10070.0313-0.1053-0.0094-0.03110.02650.06480.0155-0.0696-0.0018-0.0057-0.0153-0.04920.0088-0.01495.46548.7185.1219
35.35590.1896.64090.05130.34188.4931-0.47210.28960.3483-0.06380.07510.0341-0.57270.38460.397-0.00650.00170.00420.0096-0.0013-0.00153.50289.764212.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA67 - 1283 - 64
2X-RAY DIFFRACTION2BB67 - 1313 - 67
3X-RAY DIFFRACTION3AC - E1 - 41
4X-RAY DIFFRACTION3BF31

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