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- PDB-3q0y: N-terminal domain of C. reinhardtii SAS-6 homolog Bld12p -

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Basic information

Entry
Database: PDB / ID: 3q0y
TitleN-terminal domain of C. reinhardtii SAS-6 homolog Bld12p
ComponentsCentriole protein
KeywordsSTRUCTURAL PROTEIN / centrosome protein
Function / homology
Function and homology information


centriole / 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: 2.1 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 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: Centriole protein
D: Centriole protein
E: Centriole protein
F: Centriole protein


Theoretical massNumber of molelcules
Total (without water)108,6226
Polymers108,6226
Non-polymers00
Water20,6271145
1
A: Centriole protein
B: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2072
Polymers36,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area15640 Å2
MethodPISA
2
C: Centriole protein
D: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2072
Polymers36,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area15600 Å2
MethodPISA
3
E: Centriole protein
F: Centriole protein


Theoretical massNumber of molelcules
Total (without water)36,2072
Polymers36,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.650, 95.430, 92.010
Angle α, β, γ (deg.)90.000, 111.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Centriole protein


Mass: 18103.619 Da / Num. of mol.: 6 / Fragment: UNP residues 1-159
Source method: isolated from a genetically manipulated source
Details: PSTCM1 is derived from pET47B / 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.: 1145 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 4000, 100 MM HEPES, PH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MAR225 / Detector: CCD / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→95.55 Å / Num. obs: 82040 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 30.462 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.62
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.20.5892.6450141063699.8
2.2-2.30.4563.237646887599.8
2.3-2.60.3124.7815951918599.9
2.6-2.80.1987.236710860199.9
2.8-3.20.12411487071140999.9
3.2-40.06121.3485031140499.7
40.03731.7499041193098.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.918 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 4100 5 %RANDOM
Rwork0.1811 ---
obs0.183 82033 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.343 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 105.5 Å2 / Biso mean: 29.2879 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.2263 Å2-0 Å2-4.0158 Å2
2---6.4847 Å20 Å2
3---1.7321 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 0 1145 8082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077086
X-RAY DIFFRACTIONf_angle_d1.0289605
X-RAY DIFFRACTIONf_chiral_restr0.0691111
X-RAY DIFFRACTIONf_plane_restr0.0041247
X-RAY DIFFRACTIONf_dihedral_angle_d14.5912611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.12470.25451430.215726612804
2.1247-2.15060.30461340.21926462780
2.1506-2.17770.24281440.227727052849
2.1777-2.20640.27481400.207826852825
2.2064-2.23660.24731410.214326722813
2.2366-2.26850.24361420.204526432785
2.2685-2.30230.24941400.210727062846
2.3023-2.33820.26841400.210926252765
2.3382-2.37650.26691420.200426972839
2.3765-2.41740.23731390.201126762815
2.4174-2.46130.25141450.199626862831
2.4613-2.50850.25391360.199326732809
2.5085-2.55960.26391450.192227052850
2.5596-2.61510.25991380.195626472785
2.6151-2.67580.25071430.194326732816
2.6758-2.74260.21581410.187727022843
2.7426-2.81660.21931430.179927032846
2.8166-2.89920.20971410.173726882829
2.8992-2.99250.22951400.191426702810
2.9925-3.0990.21231440.187326952839
3.099-3.22260.22011400.180527012841
3.2226-3.36860.22221410.165126922833
3.3686-3.54530.18611440.158926922836
3.5453-3.7660.20141400.15426822822
3.766-4.05450.17581430.153827072850
4.0545-4.45840.16291410.136126992840
4.4584-5.09410.1661430.132527132856
5.0941-6.38280.18931430.179727312874
6.3828-19.91870.18281440.183627582902

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