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- PDB-3q0x: N-terminal coiled-coil dimer domain of C. reinhardtii SAS-6 homol... -

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Basic information

Entry
Database: PDB / ID: 3q0x
TitleN-terminal coiled-coil dimer domain of C. reinhardtii SAS-6 homolog Bld12p
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centrosome protein / coiled coil mediated dimer
Function / homology
Function and homology information


cytoskeleton / identical protein binding / cytoplasm
Similarity search - Function
Spindle assembly abnormal protein 6, N-terminal domain / : / Sas-6-like, oligomerization domain / Dna Repair Protein Xrcc4; Chain: A, domain 1 / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsKitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Flueckiger, I. / Goenczy, P. / Steinmetz, M.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis of the 9-fold symmetry of centrioles.
Authors: Kitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Fluckiger, I. / Gonczy, P. / Steinmetz, M.O.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)51,6292
Polymers51,6292
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-47 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.520, 79.800, 89.280
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 Centriole protein


Mass: 25814.262 Da / Num. of mol.: 2 / Fragment: UNP residues 1-226 / Mutation: F145E
Source method: isolated from a genetically manipulated source
Details: PSTCM1 pET47B derived / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6, crSAS-6 (Bld12p) / Plasmid: PSTCM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CQL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM TrisHCl, pH 8.5, 200 mM MgCl2, 20% PEG8000, 2% benzamidine, vapor diffusion, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0015 Å
DetectorType: MAR225 / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 3.02→56.29 Å / Num. obs: 10395 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 11.23 % / Biso Wilson estimate: 59.784 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.79
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3-3.10.7422.6507461962.4
3.1-3.20.6223.5905086697.9
3.2-3.30.4364.7802175998.1
3.3-3.40.3915.3667563896.8
3.4-3.50.4065.3643961197
3.5-40.2699.4273472237100
4-50.16615.226652222099.9
5-60.1515.611855998100
6-100.118.212699111099.8
100.07720.2333333799.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→56.29 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.8665 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 492 4.74 %RANDOM
Rwork0.1956 ---
obs0.1972 10390 --
Displacement parametersBiso max: 137.35 Å2 / Biso mean: 68.0898 Å2 / Biso min: 33.43 Å2
Baniso -1Baniso -2Baniso -3
1--20.2114 Å20 Å20 Å2
2---0.397 Å20 Å2
3---20.6085 Å2
Refine analyzeLuzzati coordinate error obs: 0.583 Å
Refinement stepCycle: LAST / Resolution: 3.02→56.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 0 14 3069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion20.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.02→3.38 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2584 127 4.64 %
Rwork0.2121 2611 -
all0.2145 2738 -

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