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- PDB-7x1k: Crystal structure of the flagellar expression regulator DegU from... -

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Basic information

Entry
Database: PDB / ID: 7x1k
TitleCrystal structure of the flagellar expression regulator DegU from Listeria monocytogenes
ComponentsChemotaxis protein CheY
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Chemotaxis protein CheY
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsOh, H.B. / Lee, S. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2022
Title: Structural and biochemical analyses of the flagellar expression regulator DegU from Listeria monocytogenes.
Authors: Oh, H.B. / Lee, S.J. / Yoon, S.I.
History
DepositionFeb 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheY
B: Chemotaxis protein CheY


Theoretical massNumber of molelcules
Total (without water)17,1662
Polymers17,1662
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.242, 57.242, 145.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 163 - 227 / Label seq-ID: 11 - 75

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and ((resid 163 through 164 and (name N...AA
2(chain 'B' and resid 163 through 228)BB

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Components

#1: Protein Chemotaxis protein CheY / / DNA-binding response regulator / DegU / Response regulator / Response regulator transcription ...DNA-binding response regulator / DegU / Response regulator / Response regulator transcription factor / Transcriptional regulator DegU / LuxR family / Transcriptional regulatory protein DegU


Mass: 8583.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: degU, A8L61_03890, ABZ57_11460, AF006_13045, AF817_13315, AMC55_11180, APD94_12430, ART25_12685, ARV28_13580, ARV77_08670, B1N06_09480, B1N38_12915, B1N40_06475, B1N52_12835, B1N70_00610, B1N71_ ...Gene: degU, A8L61_03890, ABZ57_11460, AF006_13045, AF817_13315, AMC55_11180, APD94_12430, ART25_12685, ARV28_13580, ARV77_08670, B1N06_09480, B1N38_12915, B1N40_06475, B1N52_12835, B1N70_00610, B1N71_10050, B1O10_09485, B1O25_07280, B2H14_13935, B4X79_11740, B4Y29_09740, B4Y40_11245, B4Y47_08610, B4Y49_10025, B4Y56_12505, B4Y57_12495, B5K54_02645, B6112_12015, B6O07_13535, BB997_11935, BCZ19_11355, BW273_12435, C6S26_09800, CW834_12940, CW845_13665, CW895_11930, CX098_09325, D4164_11095, D4271_12160, D4900_05945, D4920_11405, D4947_10625, D4C60_13755, D4D22_12850, D4D89_12585, D4U00_09980, D4U23_12680, D5M63_12150, D5N24_10760, D6P18_10065, D7104_10330, DCK28_13445, DCT16_13710, E0I39_11925, E1V33_09195, E1W43_11255, E1W56_11245, E3W32_11145, E5F58_13125, E5H26_13360, EPC87_11970, EX365_11905, EXZ73_05225, EYY39_08845, F3O35_12475, F3R75_09005, F6436_08660, F6515_06455, FA835_05775, FC284_02010, FJU19_11735, FL871_10325, FLQ97_04035, FLR03_03265, FLR11_08670, FNX31_13305, FNX40_13200, FORC68_2515, FR217_13110, FV747_11325, G3O21_002114, G3R95_002613, GEK29_13585, GF092_12975, GFK29_13135, GH165_10925, GHH22_12100, GHM39_12125, GIG92_12460, GIH49_10425, GJW51_09325, GON91_09200, GT011_13650, GXB45_06830, GYN46_05480, GYO86_13500, GYP27_09900, GYS19_01765, GYU05_06030, GYU24_13830, GYX95_10705, GYY14_10455, GYZ23_13215, GYZ33_09065, GYZ61_04015, GZI09_03780, GZK40_12260, GZM52_12045, GZN68_12600, HF764_001809, HP506_002624, HQN34_002625, KV70_11175, KW30_11950, LmNIHS28_01696, lmo2515, M643_08060, QD52_13985, R019_13750, UI29_13830, UP23_11575
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DL91
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 10058 / % possible obs: 98.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 61.14 Å2 / CC1/2: 0.998 / Net I/σ(I): 29.5
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 480 / CC1/2: 0.605 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSZ

4wsz


Resolution: 2.39→40.48 Å / SU ML: 0.3128 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 492 4.91 %
Rwork0.2267 9526 -
obs0.2281 10018 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.57 Å2
Refinement stepCycle: LAST / Resolution: 2.39→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 5 1029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771038
X-RAY DIFFRACTIONf_angle_d0.93511410
X-RAY DIFFRACTIONf_chiral_restr0.0541178
X-RAY DIFFRACTIONf_plane_restr0.0058174
X-RAY DIFFRACTIONf_dihedral_angle_d16.02619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.630.37871200.30172317X-RAY DIFFRACTION99.07
2.63-3.010.31141110.2732360X-RAY DIFFRACTION98.88
3.01-3.790.27381180.24622373X-RAY DIFFRACTION98.65
3.79-40.480.22291430.19932476X-RAY DIFFRACTION97.11
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)
18.33818845023-1.74201165189-1.317769438554.64805686121.530476080696.7115307934-0.248163830446-0.707820892857-0.6728521045480.362181486478-0.01346518414130.4526952053870.4130271936220.4739163280380.1481896295180.404256895847-0.01565032678420.03515681378610.5226022266830.1281622134350.39515864976878.3437034058-41.70966918386.96359590462
29.38911125534-3.33467920972.770956014439.48408788443-4.791036208322.56687236363-0.1317248859431.03363490951-0.214283590355-0.808777869959-0.349932779264-0.0694470487507-0.01653615317921.965191960380.3716709421040.5142615260820.0133743616047-0.04743990292080.9624301795750.05759967997660.54058691895390.1017225367-39.68640279699.50903524301
34.128015209410.31193209359-4.179501158934.089831650912.970312576386.88116827439-1.14350495845-1.61479385102-0.9678442745112.04291807517-0.493991109348-0.54525950422-1.373756492350.2308988452731.106555930890.6703998835440.0883301792614-0.05934049835191.171217656070.2224958068460.43262012668682.7865956946-38.436038921318.5068706679
43.984757479030.3255339725393.756765395957.37400813052.369758026964.17611594742-0.3230473202861.514377476030.0577116493248-0.00510355085740.1917096110090.775416350849-0.1955079342360.7351432030680.4626415746920.519348176875-0.106791188118-0.01172405185670.8528090117990.08447976918270.671464034831100.362732662-52.514130068518.0526091017
57.70230465909-0.258421491961-1.652221435122.13187808510.5048898164437.63106441852-0.5480797171882.2534683577-0.929909609087-0.839259415460.205511703424-0.05860963077880.08639273771161.059537305220.07519858401090.822277158891-0.0872003559122-0.04639241332811.28451688241-0.08263458594780.714405886953101.375252588-53.98193931849.1518319603
66.457668261861.735712713151.188996902272.250207109310.1963421219626.92145980801-0.01807513775861.096698721480.007108948182660.459672471371-0.7195214593430.5367402757680.09305197827730.5173600038570.605449145420.529830693786-0.00648714483737-0.02863287966620.6568356544760.005578583228110.68606212801491.3878811191-49.511524202417.8405134304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 207 )
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 228 )
4X-RAY DIFFRACTION4chain 'B' and (resid 161 through 178 )
5X-RAY DIFFRACTION5chain 'B' and (resid 179 through 207 )
6X-RAY DIFFRACTION6chain 'B' and (resid 208 through 228 )

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