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- PDB-5y6g: PilZ domain with c-di-GMP of YcgR from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5y6g
TitlePilZ domain with c-di-GMP of YcgR from Escherichia coli
ComponentsFlagellar brake protein YcgR
KeywordsPROTEIN BINDING / C-di-GMP binding / PilZ domain / Flagellar brake protein
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)18,6334
Polymers17,1561
Non-polymers1,4773
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.340, 110.340, 35.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 17155.709 Da / Num. of mol.: 1 / Fragment: UNP residues 112-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (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-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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2015
RadiationMonochromator: DOUBLE CRYSTAL (SI 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→47.78 Å / Num. obs: 11266 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.031 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1624 / CC1/2: 0.875 / Rpim(I) all: 0.203 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y6F

5y6f


Resolution: 2.3→47.779 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2283 504 4.48 %
Rwork0.2037 --
obs0.2048 11252 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 97 45 1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021200
X-RAY DIFFRACTIONf_angle_d0.5581639
X-RAY DIFFRACTIONf_dihedral_angle_d16.884678
X-RAY DIFFRACTIONf_chiral_restr0.035175
X-RAY DIFFRACTIONf_plane_restr0.003196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.53160.291420.23952645X-RAY DIFFRACTION100
2.5316-2.89790.32461040.23852687X-RAY DIFFRACTION100
2.8979-3.65090.19721140.19032691X-RAY DIFFRACTION100
3.6509-47.78890.21261440.19482725X-RAY DIFFRACTION99
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)
11.8810.3955-1.53531.15530.21931.7060.27630.099-0.18850.0344-0.0452-0.1128-0.21070.21970.02390.233-0.066-0.00940.4205-0.09910.3067-41.072934.0388-18.467
22.0566-0.3070.12350.6710.77240.72150.12010.254-0.08420.09450.162-0.0468-0.19450.51080.31320.2368-0.23410.06930.4675-0.05230.1885-38.678439.1691-19.3164
30.272-0.0171-0.08290.8640.41010.26640.0686-0.0696-0.81150.18610.3477-0.46510.70880.930.1590.4510.1617-0.15130.7174-0.21490.8622-30.245721.9892-18.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 112 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 242 )

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