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- PDB-5vx6: Structure of Bacillus subtilis Inhibitor of motility (MotI/DgrA) -

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Basic information

Entry
Database: PDB / ID: 5vx6
TitleStructure of Bacillus subtilis Inhibitor of motility (MotI/DgrA)
ComponentsUncharacterized protein YpfA
KeywordsGMP BINDING PROTEIN / c-di-GMP / YcgR / MotI / PilZ / DgrA / YpfA / motility
Function / homologyFlagellar protein YcgR / Type III secretion system flagellar brake protein YcgR, PilZN domain / PilZ domain / PilZ domain / cyclic-di-GMP binding / Chem-C2E / Uncharacterized protein YpfA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.197 Å
AuthorsSubramanian, S. / Dann III, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM093030 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: MotI (DgrA) acts as a molecular clutch on the flagellar stator protein MotA inBacillus subtilis.
Authors: Subramanian, S. / Gao, X. / Dann 3rd., C.E. / Kearns, D.B.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YpfA
B: Uncharacterized protein YpfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4956
Polymers49,7332
Non-polymers2,7624
Water0
1
A: Uncharacterized protein YpfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2483
Polymers24,8671
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein YpfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2483
Polymers24,8671
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.410, 75.410, 402.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein YpfA


Mass: 24866.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ypfA, jofA, BSU22910 / Production host: Escherichia coli (E. coli) / References: UniProt: P38491
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23- 24 % PEG3350 0.1M Bis-Tris Propane pH-6.5 0.2M Na-K tartarate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9763 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 18, 2015
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.197→50 Å / Num. obs: 11077 / % possible obs: 98.9 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.036 / Net I/σ(I): 17
Reflection shellResolution: 3.197→3.26 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 559 / CC1/2: 0.925 / Rpim(I) all: 0.152 / Rsym value: 0.378 / Χ2: 0.833 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.197→46.793 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 1111 10.03 %Random selection
Rwork0.236 ---
obs0.2402 11077 90.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.197→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 0 3379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043438
X-RAY DIFFRACTIONf_angle_d0.8614702
X-RAY DIFFRACTIONf_dihedral_angle_d16.5842094
X-RAY DIFFRACTIONf_chiral_restr0.054558
X-RAY DIFFRACTIONf_plane_restr0.003577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1967-3.34220.4044780.349696X-RAY DIFFRACTION53
3.3422-3.51830.33861260.29681129X-RAY DIFFRACTION85
3.5183-3.73870.32081430.28391297X-RAY DIFFRACTION97
3.7387-4.02720.3011450.26271283X-RAY DIFFRACTION97
4.0272-4.43220.28071470.22891338X-RAY DIFFRACTION98
4.4322-5.07290.23491500.19031333X-RAY DIFFRACTION98
5.0729-6.38870.26421550.23141391X-RAY DIFFRACTION99
6.3887-46.79770.23811670.20171499X-RAY DIFFRACTION98

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