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- PDB-6if6: Structure of the periplasmic domain of SflA -

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Basic information

Entry
Database: PDB / ID: 6if6
TitleStructure of the periplasmic domain of SflA
ComponentsProtein SflA
KeywordsMEMBRANE PROTEIN / Flagellar formation control / single transmembrane protein
Function / homologyChaperone J-domain superfamily / DnaJ domain / Tetratricopeptide-like helical domain superfamily / PHOSPHATE ION / DnaJ domain protein
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNishikawa, S. / Sakuma, M. / Kojima, S. / Homma, M. / Imada, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H02386 Japan
Japan Society for the Promotion of ScienceJP16H04774 Japan
CitationJournal: J.Biochem. / Year: 2019
Title: Structure of the periplasmic domain of SflA involved in spatial regulation of the flagellar biogenesis of Vibrio reveals a TPR/SLR-like fold.
Authors: Sakuma, M. / Nishikawa, S. / Inaba, S. / Nishigaki, T. / Kojima, S. / Homma, M. / Imada, K.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 27, 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: Protein SflA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3643
Polymers15,1771
Non-polymers1872
Water86548
1
A: Protein SflA
hetero molecules

A: Protein SflA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7276
Polymers30,3532
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 66.900, 59.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein Protein SflA


Mass: 15176.550 Da / Num. of mol.: 1 / Fragment: periplasmic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1W6TB41*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-terminal HM is remnant of the His-tag.

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES-NaOH pH 7.5, 0.8M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→21.9 Å / Num. obs: 12475 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 833 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→21.898 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93
RfactorNum. reflection% reflection
Rfree0.2207 1228 9.86 %
Rwork0.1761 --
obs0.1804 12457 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→21.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 11 48 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091082
X-RAY DIFFRACTIONf_angle_d1.0781470
X-RAY DIFFRACTIONf_dihedral_angle_d16.429401
X-RAY DIFFRACTIONf_chiral_restr0.049154
X-RAY DIFFRACTIONf_plane_restr0.006200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8972-1.97310.32251360.23341226X-RAY DIFFRACTION98
1.9731-2.06290.23381270.18961221X-RAY DIFFRACTION100
2.0629-2.17150.22991310.17611254X-RAY DIFFRACTION100
2.1715-2.30740.21681360.16821246X-RAY DIFFRACTION99
2.3074-2.48540.24521350.18391232X-RAY DIFFRACTION98
2.4854-2.73510.20841390.1911227X-RAY DIFFRACTION100
2.7351-3.12980.27551410.18911252X-RAY DIFFRACTION99
3.1298-3.93950.19951360.16711249X-RAY DIFFRACTION97
3.9395-21.89960.19361470.16091322X-RAY DIFFRACTION99

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