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- PDB-5y6f: Crystal structure of YcgR in complex with c-di-GMP from Escherich... -

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Basic information

Entry
Database: PDB / ID: 5y6f
TitleCrystal structure of YcgR in complex with c-di-GMP from Escherichia coli
ComponentsFlagellar brake protein YcgR
KeywordsPROTEIN BINDING / C-di-GMP binding / Flagellar brake protein / Motor protein binding / PilZ domain
Function / homology
Function and homology information


regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed / negative regulation of bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body / cyclic-di-GMP binding / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Type III secretion system flagellar brake protein YcgR / Flagellar regulator YcgR, PilZN domain / Type III secretion system flagellar brake protein YcgR, PilZN domain / PilZ domain / PilZ domain / FMN-binding split barrel
Similarity search - Domain/homology
Chem-C2E / Flagellar brake protein YcgR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHou, Y.J. / Wang, D.C. / Li, D.F.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility inEscherichia coli.
Authors: Hou, Y.J. / Yang, W.S. / Hong, Y. / Zhang, Y. / Wang, D.C. / Li, D.F.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _citation_author.identifier_ORCID
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Flagellar brake protein YcgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8964
Polymers29,4191
Non-polymers1,4773
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.980, 93.980, 109.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Flagellar brake protein YcgR / Cyclic di-GMP binding protein YcgR


Mass: 29418.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ycgR, b1194, JW1183 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76010
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M potassium thiocyanate, 0.1M Bis-Tris pH 6.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→46.99 Å / Num. obs: 15972 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.026 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2357 / CC1/2: 0.818 / Rpim(I) all: 0.232 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMv.7.0.4data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.99 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2334 774 4.85 %
Rwork0.1829 --
obs0.1855 15972 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 97 42 1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121973
X-RAY DIFFRACTIONf_angle_d1.382691
X-RAY DIFFRACTIONf_dihedral_angle_d17.2361136
X-RAY DIFFRACTIONf_chiral_restr0.065300
X-RAY DIFFRACTIONf_plane_restr0.008327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.44420.28951140.2252564X-RAY DIFFRACTION100
2.4442-2.63290.2511300.20042535X-RAY DIFFRACTION100
2.6329-2.89780.26481150.21682553X-RAY DIFFRACTION100
2.8978-3.3170.27151430.19792550X-RAY DIFFRACTION100
3.317-4.17870.22081460.17382525X-RAY DIFFRACTION100
4.1787-46.99980.21211260.16852471X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.83291.47323.91243.49752.0446.2585-0.31570.26330.4511-0.7508-0.09060.6458-0.4807-0.61260.33520.471-0.0102-0.07020.4111-0.01980.4776-21.2627-0.95479.6136
24.70450.41331.5354.03940.86175.4325-0.0429-0.2502-0.87430.41660.02180.14970.7795-0.0819-0.0660.4086-0.04720.1120.34720.01530.4615-9.3566-13.381125.6318
34.77072.4958-3.28746.9582-1.46582.2993-0.4968-1.3377-1.54291.14250.02221.09070.3146-0.99360.62090.9298-0.15340.18161.1910.36040.9667-18.1871-19.961439.0982
46.666-0.8894-1.85078.49131.09075.4216-0.231-1.214-1.41591.4171-0.78980.47770.55210.38520.74710.823-0.02960.33491.02960.29341.0154-16.9293-17.250238.3145
57.4668-2.261-1.78926.33891.62435.2244-0.0086-0.4263-0.77820.71980.1294-0.26570.847-0.0903-0.04560.6832-0.124-0.01360.48910.24920.5468-4.5798-22.518630.2389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 243 )

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