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- PDB-5ar1: Crystal structure of Cdc11 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5ar1
TitleCrystal structure of Cdc11 from Saccharomyces cerevisiae
ComponentsCELL DIVISION CONTROL PROTEIN 11
KeywordsCELL CYCLE / SPETINS / YEAST / CDC11 / NUCLEOTIDE BINDING
Function / homology
Function and homology information


septin filament array / cellular bud neck septin ring organization / protein localization to bud neck / ascospore wall / mating projection base / cellular bud neck septin ring / protein localization => GO:0008104 / actomyosin contractile ring assembly / septin complex / prospore membrane ...septin filament array / cellular bud neck septin ring organization / protein localization to bud neck / ascospore wall / mating projection base / cellular bud neck septin ring / protein localization => GO:0008104 / actomyosin contractile ring assembly / septin complex / prospore membrane / Release of apoptotic factors from the mitochondria / cytoskeleton-dependent cytokinesis / phosphatidylinositol-5-phosphate binding / maintenance of cell polarity / septin ring / cellular bud neck / mating projection tip / division septum assembly / phosphatidylinositol-4-phosphate binding / meiotic spindle / cell division site / cytoplasmic microtubule / mitotic cytokinesis / positive regulation of protein kinase activity / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton / molecular adaptor activity / GTPase activity / GTP binding / identical protein binding
Similarity search - Function
Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 11
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBrausemann, A. / Gerhardt, S. / Schott, A.K. / Einsle, O. / Grosse-Berkenbusch, A. / Johnsson, N. / Gronemeyer, T.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal Structure of Cdc11, a Septin Subunit from Saccharomyces Cerevisiae.
Authors: Brausemann, A. / Gerhardt, S. / Schott, A.K. / Einsle, O. / Grosse-Berkenbusch, A. / Johnsson, N. / Gronemeyer, T.
History
DepositionSep 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 29, 2017Group: Other
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
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 / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL DIVISION CONTROL PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)34,6121
Polymers34,6121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.050, 187.050, 57.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein CELL DIVISION CONTROL PROTEIN 11 / SEPTIN


Mass: 34611.719 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32458
Sequence detailsN-TERMINAL 6-HIS TAG INCL. TEV CLEAVAGE SITE

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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: 4.23 Å3/Da / Density % sol: 70.91 %
Crystal growpH: 5.5 / Details: PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.85→162 Å / Num. obs: 14458 / % possible obs: 99.9 % / Redundancy: 34.1 % / Biso Wilson estimate: 95.73 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 21.5
Reflection shellResolution: 2.85→3 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1 / Rsym value: 1.052 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
autoPROCdata reduction
XDS(VERSION MARCH 1data reduction
Aimless(VERSION 0.5.14)data scaling
CCP46.5.data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QNR

2qnr


Resolution: 2.85→34.2 Å / Cor.coef. Fo:Fc: 0.9172 / Cor.coef. Fo:Fc free: 0.9262 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.249
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 682 4.73 %RANDOM
Rwork0.2573 ---
obs0.2574 14431 99.84 %-
Displacement parametersBiso mean: 167.47 Å2
Baniso -1Baniso -2Baniso -3
1--10.3678 Å20 Å20 Å2
2---10.3678 Å20 Å2
3---20.7356 Å2
Refine analyzeLuzzati coordinate error obs: 1.433 Å
Refinement stepCycle: LAST / Resolution: 2.85→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 0 1643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011667HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.22261HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d562SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes241HARMONIC5
X-RAY DIFFRACTIONt_it1667HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion25.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion237SEMIHARMONIC5
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_contact1859SEMIHARMONIC4
LS refinement shellResolution: 2.85→3.08 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2404 128 4.43 %
Rwork0.2437 2764 -
all0.2436 2892 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: -23.6531 Å / Origin y: -75.2125 Å / Origin z: 16.1124 Å
111213212223313233
T-0.8459 Å20.0748 Å20.0669 Å2-0.796 Å20.2347 Å2---0.2186 Å2
L7.2975 °2-0.8627 °2-2.55 °2-4.0112 °20.3038 °2--11.0841 °2
S-0.0053 Å °0.481 Å °0.3099 Å °-0.2452 Å °-0.2157 Å °-0.8703 Å °-0.8877 Å °2.6478 Å °0.221 Å °
Refinement TLS groupSelection details: { A|* }

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