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- PDB-5y6h: Crystal structure of YcgR-N domain of YcgR from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5y6h
TitleCrystal structure of YcgR-N domain of YcgR from Escherichia coli
ComponentsFlagellar brake protein YcgR
KeywordsUNKNOWN FUNCTION / YcgR-N domain / YcgR / 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
Flagellar brake protein YcgR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.774 Å
AuthorsHou, Y.J. / Yang, W.S. / 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 / 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 / _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


Theoretical massNumber of molelcules
Total (without water)13,4831
Polymers13,4831
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6830 Å2
Unit cell
Length a, b, c (Å)91.960, 91.960, 32.530
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: 13483.472 Da / Num. of mol.: 1 / Fragment: UNP residues 1-111
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MES pH 5.6, 0.01M Magnesium chloride hexahydrate, 1.8M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→30.11 Å / Num. obs: 9774 / % possible obs: 98.5 % / Redundancy: 11 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Net I/σ(I): 26.6
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 7 / Num. unique obs: 1396 / CC1/2: 0.962 / Rpim(I) all: 0.1 / % possible all: 97.6

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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: 1.774→16.982 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.48
RfactorNum. reflection% reflection
Rfree0.1932 976 10 %
Rwork0.1713 --
obs0.1736 9762 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.774→16.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 0 94 964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004890
X-RAY DIFFRACTIONf_angle_d0.771215
X-RAY DIFFRACTIONf_dihedral_angle_d8.266534
X-RAY DIFFRACTIONf_chiral_restr0.048145
X-RAY DIFFRACTIONf_plane_restr0.005154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.774-1.86740.2441400.20991230X-RAY DIFFRACTION98
1.8674-1.98430.23981340.18711253X-RAY DIFFRACTION98
1.9843-2.13720.21471400.17721237X-RAY DIFFRACTION98
2.1372-2.35180.21071380.17681258X-RAY DIFFRACTION98
2.3518-2.69090.19361400.18541273X-RAY DIFFRACTION99
2.6909-3.38580.20241420.17621263X-RAY DIFFRACTION99
3.3858-16.98250.16151420.15181272X-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)
12.0002-1.13080.60941.2185-0.80780.64870.2937-0.66751.97260.7559-0.03-0.3137-1.3981-1.1828-0.09850.8633-0.00180.15130.7624-0.02330.3425-7.9018-17.33719.3823
20.8969-0.0401-0.65771.7401-0.05640.38830.2173-0.112-0.332-0.2057-0.07350.2290.3176-0.3617-0.02860.1385-0.0305-0.03680.20410.02760.1933-9.58-26.32836.9009
30.2685-0.0421-0.32650.01960.01850.6321-0.3157-0.08490.90780.05180.19610.2156-0.27320.24260.00080.1836-0.0358-0.03460.2521-0.00560.21072.3234-14.25662.2728
40.3347-0.1159-0.29890.10150.20860.8895-0.00690.04970.2103-0.04240.12440.0635-0.1402-0.1175-0.00040.157-0.0292-0.01130.17790.02410.2081-0.5331-20.6241-0.7256
50.6538-0.02370.37240.65460.56810.8373-0.05250.09790.1020.02760.1141-0.0531-0.10640.08960.00020.1579-0.02330.00440.18730.01250.15387.0326-21.4172-1.7786
60.374-0.0991-0.26060.29950.43271.1711-0.6685-0.66340.23810.28750.3532-0.0659-0.1320.037-0.010.18220.0329-0.03390.24380.01230.24112.304-16.18697.0533
70.1566-0.2559-0.44870.30220.46420.8519-0.2948-0.60960.46650.0960.1785-0.3492-0.2728-0.16530.00030.21460.0122-0.03030.1807-0.00680.1812-5.0335-15.60928.7509
80.32530.2211-0.04870.9823-0.46720.17380.3908-0.4291-0.16640.3889-0.05010.04151.0444-0.7070.01020.3364-0.06820.00980.3926-0.01980.27586.3686-28.2341-2.4926
90.81840.11760.56510.1056-0.31411.1123-0.0232-0.06620.03990.003-0.026-0.0788-0.132-0.3845-0.00080.18580.019-0.02710.2827-0.0140.1848-1.8848-21.59947.847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 36 )
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 47 )
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 67 )
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 77 )
7X-RAY DIFFRACTION7chain 'A' and (resid 78 through 86 )
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 96 )
9X-RAY DIFFRACTION9chain 'A' and (resid 97 through 113 )

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