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- PDB-4ckm: Structure of the N-terminal domain of Leishmania SAS-6 -

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Basic information

Entry
Database: PDB / ID: 4ckm
TitleStructure of the N-terminal domain of Leishmania SAS-6
ComponentsSAS-6
KeywordsSTRUCTURAL PROTEIN / BASAL BODY / CENTRIOLE / CARTWHEEL / TRYPANOSOMATIDS
Function / homology
Function and homology information


centriole replication / centriole / ciliary basal body / cytoplasm
Similarity search - Function
SAS-6, C-terminal coiled coil / : / Spindle assembly abnormal protein 6, N-terminal 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
Uncharacterized protein
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
Authorsvan Breugel, M.
CitationJournal: Elife / Year: 2014
Title: Structure of the SAS-6 cartwheel hub from Leishmania major.
Authors: van Breugel, M. / Wilcken, R. / McLaughlin, S.H. / Rutherford, T.J. / Johnson, C.M.
History
DepositionJan 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Jan 17, 2018Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAS-6
B: SAS-6
C: SAS-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1826
Polymers59,0413
Non-polymers1413
Water2,756153
1
A: SAS-6

A: SAS-6


Theoretical massNumber of molelcules
Total (without water)39,3612
Polymers39,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area1490 Å2
ΔGint-7.6 kcal/mol
Surface area15160 Å2
MethodPISA
2
B: SAS-6
C: SAS-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5015
Polymers39,3612
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-19.3 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.250, 84.250, 239.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.00687, 0.3062, -0.9519), (-0.7846, -0.5919, -0.1847), (-0.62, 0.7456, 0.2443)309.2, 201.6, 176
2given(-0.8694, -0.4361, -0.2325), (-0.007432, 0.482, -0.8761), (0.4941, -0.76, -0.4223)212.3, 279.4, 360.9

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Components

#1: Protein SAS-6


Mass: 19680.324 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 97-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Description: SYNTHETIC GENE / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E9AFQ5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.5 Å3/Da / Density % sol: 65 %
Description: STRUCTURE WAS SOLVED BY MAD USING A DATASET OBTAINED FROM CRYSTALS OF THE SELENOMETHIONINE DERIVATIVE.
Crystal growpH: 5.1
Details: 100 MM BISTRIS PH 5.1, 200 MM MGCL2, 20% (W/V) PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→48.86 Å / Num. obs: 48008 / % possible obs: 99.9 % / Observed criterion σ(I): 1.4 / Redundancy: 5.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0047refinement
MOSFLMdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.15→79.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.924 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24534 2398 5 %RANDOM
Rwork0.20839 ---
obs0.21024 45569 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.513 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.15→79.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 8 153 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193466
X-RAY DIFFRACTIONr_bond_other_d0.0010.023337
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9924731
X-RAY DIFFRACTIONr_angle_other_deg0.70137658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43523.252163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22115570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6851531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.2190.2681
X-RAY DIFFRACTIONr_nbd_other0.1720.23317
X-RAY DIFFRACTIONr_nbtor_refined0.180.21688
X-RAY DIFFRACTIONr_nbtor_other0.0830.21996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1030.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1225.0071702
X-RAY DIFFRACTIONr_mcbond_other3.1165.0031701
X-RAY DIFFRACTIONr_mcangle_it5.0687.4842122
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4945.3751764
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7167.9352606
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 184 -
Rwork0.355 3307 -
obs--100 %

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