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- PDB-6wsm: Crystal structure of coiled coil region of human septin 8 -

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Basic information

Entry
Database: PDB / ID: 6wsm
TitleCrystal structure of coiled coil region of human septin 8
ComponentsSeptin-8
KeywordsSTRUCTURAL PROTEIN / Coiled coil / Septin
Function / homology
Function and homology information


regulation of SNARE complex assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / regulation of intracellular protein transport / regulation of protein stability / protein localization / synaptic vesicle membrane / microtubule cytoskeleton ...regulation of SNARE complex assembly / septin complex / cytoskeleton-dependent cytokinesis / septin ring / cell division site / regulation of intracellular protein transport / regulation of protein stability / protein localization / synaptic vesicle membrane / microtubule cytoskeleton / presynapse / molecular adaptor activity / axon / GTPase activity / GTP binding
Similarity search - Function
Septin 8 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.451 Å
AuthorsCabrejos, D.A.L. / Cavini, I. / Sala, F.A. / Valadares, N.F. / Pereira, H.M. / Brandao-Neto, J. / Nascimento, A.F.Z. / Uson, I. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/04658-9 Brazil
Sao Paulo Research Foundation (FAPESP)2018/19992-7 Brazil
Sao Paulo Research Foundation (FAPESP)2015/00062-1 Brazil
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Orientational Ambiguity in Septin Coiled Coils and its Structural Basis.
Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H. ...Authors: Leonardo, D.A. / Cavini, I.A. / Sala, F.A. / Mendonca, D.C. / Rosa, H.V.D. / Kumagai, P.S. / Crusca Jr., E. / Valadares, N.F. / Marques, I.A. / Brandao-Neto, J. / Munte, C.E. / Kalbitzer, H.R. / Soler, N. / Uson, I. / Andre, I. / Araujo, A.P.U. / D'Muniz Pereira, H. / Garratt, R.C.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5774
Polymers15,2891
Non-polymers2883
Water30617
1
A: Septin-8
hetero molecules

A: Septin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1558
Polymers30,5782
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area3880 Å2
ΔGint-92 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.007, 92.007, 56.769
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-216-

HOH

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Components

#1: Protein Septin-8 /


Mass: 15289.100 Da / Num. of mol.: 1 / Fragment: coiled coil region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN8, KIAA0202, SEPT8 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q92599
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 100mM Citric acid, 1.25M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 2.45→56.77 Å / Num. obs: 5585 / % possible obs: 100 % / Redundancy: 37.1 % / Biso Wilson estimate: 39.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.018 / Rrim(I) all: 0.109 / Net I/σ(I): 15 / Num. measured all: 207457 / Scaling rejects: 647
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.5538.51.873231546010.9870.3041.8981.6100
8.83-56.7727.70.03446116110.0060.03162.499.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
STARANISOdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.451→46.235 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.8
RfactorNum. reflection% reflection
Rfree0.3389 377 10.23 %
Rwork0.3185 --
obs0.3207 3684 66.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.21 Å2 / Biso mean: 69.2468 Å2 / Biso min: 28.87 Å2
Refinement stepCycle: final / Resolution: 2.451→46.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 15 17 587
Biso mean--109.93 52.59 -
Num. residues----74
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001570
X-RAY DIFFRACTIONf_angle_d0.321766
X-RAY DIFFRACTIONf_chiral_restr0.02687
X-RAY DIFFRACTIONf_plane_restr0.001100
X-RAY DIFFRACTIONf_dihedral_angle_d16.715357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4514-2.80610.4604620.405346830
2.8061-3.53520.33151280.3328111968
3.5352-46.2250.32841870.3056172098
Refinement TLS params.Method: refined / Origin x: 30.066 Å / Origin y: 44.807 Å / Origin z: 54.564 Å
111213212223313233
T0.353 Å20.5799 Å2-0.2592 Å2-0.8393 Å20.1663 Å2--0.1317 Å2
L0.3204 °20.016 °20.6125 °2-0.3531 °2-0.2342 °2--1.9258 °2
S0.1316 Å °0.0691 Å °0.0164 Å °-0.2048 Å °-0.0691 Å °-0.0706 Å °-0.0291 Å °-0.0627 Å °0.0882 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 335:408 )

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