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- PDB-7od9: Crystal structure of activated CheY fused to the C-terminal domai... -

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Basic information

Entry
Database: PDB / ID: 7od9
TitleCrystal structure of activated CheY fused to the C-terminal domain of CheF
Components
  • C-terminal domain of CheF from Methanococcus maripaludis
  • Response regulator receiver protein
KeywordsMETAL BINDING PROTEIN / archaellum / chemotaxis / phosphorylation / motility
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Taxis protein CheF1/F2 / Chemotaxis signal transduction system protein F from archaea / 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
BERYLLIUM TRIFLUORIDE ION / Response regulator receiver protein / Uncharacterized protein
Similarity search - Component
Biological speciesMethanococcus maripaludis X1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAltegoer, F. / Weiland, P. / Bange, G.
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into the mechanism of archaellar rotational switching.
Authors: Altegoer, F. / Quax, T.E.F. / Weiland, P. / Nussbaum, P. / Giammarinaro, P.I. / Patro, M. / Li, Z. / Oesterhelt, D. / Grininger, M. / Albers, S.V. / Bange, G.
History
DepositionApr 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Response regulator receiver protein
A: Response regulator receiver protein
C: C-terminal domain of CheF from Methanococcus maripaludis
F: C-terminal domain of CheF from Methanococcus maripaludis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7928
Polymers56,6114
Non-polymers1814
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-72 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 70.870, 59.820
Angle α, β, γ (deg.)90.000, 91.603, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Response regulator receiver protein / CheY from Methanococcus maripaludis


Mass: 15673.263 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis X1 (archaea) / Gene: GYY_05385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0H061
#2: Protein C-terminal domain of CheF from Methanococcus maripaludis


Mass: 12632.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis X1 (archaea) / Gene: GYY_05390 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0H062
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 MgCl2, 0.1 M Tris pH 8.5, 20 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→44.07 Å / Num. obs: 20987 / % possible obs: 99.61 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.86 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.66
Reflection shellResolution: 2.3→2.383 Å / Mean I/σ(I) obs: 0.88 / Num. unique obs: 2097 / CC1/2: 0.577

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EKH

6ekh


Resolution: 2.3→44.07 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.0381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3066 1043 4.98 %
Rwork0.2495 19888 -
obs0.2524 20931 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 10 83 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513325
X-RAY DIFFRACTIONf_angle_d0.86414482
X-RAY DIFFRACTIONf_chiral_restr0.0476539
X-RAY DIFFRACTIONf_plane_restr0.0065572
X-RAY DIFFRACTIONf_dihedral_angle_d15.9538434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.47061470.47882790X-RAY DIFFRACTION99.63
2.42-2.570.44761490.40852848X-RAY DIFFRACTION99.63
2.57-2.770.3891470.36212815X-RAY DIFFRACTION99.7
2.77-3.050.35221480.30462826X-RAY DIFFRACTION99.6
3.05-3.490.33051490.24872859X-RAY DIFFRACTION99.73
3.49-4.40.27941500.19582853X-RAY DIFFRACTION99.7
4.4-45.70.24061530.19792897X-RAY DIFFRACTION99.35
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)
10.1652194821190.2490107814790.1072646425660.167947630078-0.02064700112470.230867752080.383795308258-0.6475701175820.2210973770131.14109696065-0.264284428595-0.6568339812440.2138255434770.1335193854150.0003917142756880.91462282844-0.0379601128640.002612402555980.63806552565-0.05260429837260.62261076019125.18006231074.2569304381629.8704272654
20.7926125182391.655433091250.6065203373434.02437342141.192044422270.479346128136-0.8845600913990.562216623819-0.669690896162-0.00587778481340.556356455238-1.58560160529-0.982839519873-0.714465962725-0.09808483423311.32293140497-0.05127657597150.1603518563951.22192442882-0.2669774171130.6722824144493.3317144326710.5526965937-15.5809095063
31.341775103950.379892045252-0.356646055159-0.00731376588915-0.128961799260.3094125425170.341450184535-0.02632152891390.220367844275-0.8429025105680.120372928483-0.473116013538-1.11576645783-1.561172944760.02285600276290.9556917356170.0678903258063-0.08174359928340.7132001091420.04541217507450.7527220222779.9291738335519.4154963511-4.15329057459
40.5972357229710.456775501354-0.5449952109210.568230019631-0.1915089244970.543336695749-0.185774863215-0.33719040065-0.0973584144489-0.350117741384-0.05397367515940.1890785923560.156250306114-0.5307015321560.0004853591670970.9053631895060.1933768218280.03465744078650.854398578268-0.04977119025170.7187025609757.3588193740717.28659590029.62098988913
50.8607984256540.1698755114110.4390363145010.5856306352460.7658208337080.575046389464-0.169641596514-0.3473418494110.2582440237060.2158554654170.192865601805-0.1528341826320.0531463652386-1.057824669540.0003443657290790.977124754023-0.007697110024530.107218501280.909626526923-0.032550456980.7862605295751.078322532577.044237793223.7013307594
60.962583078589-0.103164811984-0.9014819605951.06240367844-0.1048516662910.567482823441-0.006206862352520.0139148687978-0.19254854258-0.0377330663337-0.155803918988-0.0186155885973-0.4786129709360.0267253963989-6.08918008848E-60.820646887028-0.07467702486240.07517944317871.04295995242-0.06471095055230.688872126544-2.113491304572.8791891153226.2795340016
70.848927822017-1.06924584714-0.01516075895251.145331181310.2910572349170.518215409728-0.2800393711270.254032159752-0.482896925905-0.1144648044140.07109014741820.03358627749270.377039430397-0.2576468959720.0001989167822450.831154465716-0.0419687879562-0.06538054861530.6156717018610.01544134139980.6938146022348.9334940495113.221192216-3.58966482617
81.67069046810.278276425678-0.1160755702830.00366579654602-0.0004232055107260.4790412285740.4868954477-0.192515361605-0.01134886907660.388092426608-0.2366027848250.8144683452490.5068949225390.2415677303070.0004488069380450.685639762948-0.049108593435-0.04792037302740.584110127180.00679583534280.52866277028528.6870218030.5863799282336.84476321991
90.0160028224917-0.00570528057644-0.02823901779740.2002474681640.1986810191850.1161065270250.0571130122196-0.3603948549240.301115150051.381643367260.5364663459780.2709436028450.3869136645510.3775169625410.0001972968293310.7581671411150.144843456772-0.01939523139480.620947096602-0.03902248078750.56988533115320.59984932018.219662597147.27919111596
100.330091058839-0.511287192682-0.1023440762631.4500769292-0.4850326532632.347748143760.0133490173215-0.225372828525-0.1636450290110.507797479414-0.0987574199784-0.0251183365573-0.6601812200260.08571739539670.1580634998240.1941492010360.0640033103026-0.06499066573680.482062386901-0.0003959307233810.58424977291833.21800594423.909843767876.26299996543
110.227860678175-0.384659125537-0.3359799511980.2305990539460.5514742741370.630728227510.06851485008630.390617046846-0.05373004199460.0294870776991-0.281610770409-0.0817473079617-0.1536646093550.164080996020.0002952184877280.4104761394370.0434137010771-0.01568832488820.5662993321850.02801537328580.59165875988435.0371875814.19611395834-3.82602039515
120.198285962910.1545628280070.2165677128180.06675975087980.08975822492710.395955940970.4864609789270.3012808851540.531410579958-0.902339220581-0.350745631231-0.297821834377-0.2751788190220.02510783951370.0009828556007161.029089133320.09804594174650.05507218006570.676570962827-0.004387777942790.61084721044528.03173986343.47285939753-14.4007801605
130.3174671503010.1101590555360.005019517003440.203449176849-0.1617090848120.2476625066190.09798743687240.304494396291-0.1059264721860.3557153598650.31690517489-0.529678229489-0.222461158041-0.4409671766470.275506971857-0.862990145541-0.028659945035-0.4198804348330.6564548299460.109555765220.64329280873521.91528705092.45734185024-5.31968665758
14-0.156224014550.00232542686852-0.1044749828610.08785259487870.04009996682380.15400768069-0.147391366158-0.293880754607-0.0604944139275-0.558681960330.318705601476-0.03555392771030.147929591793-0.3245609292660.0008972693411050.955860405902-0.0559047868403-0.04085269821430.570319078781-0.04190719220330.61453325986121.4801052089-9.67499462194.09446446179
150.219030146922-0.1214942250520.2138216012220.506749984999-0.1062347489550.1973493672430.4107685628880.554103690944-0.9432636385171.1907795816-0.337428087508-0.7396926281150.0830035026586-0.239385515844-0.0004871668196520.76663181955-0.104810030143-0.003944592845170.490179515629-0.1083700621090.59231319880921.7445456851-7.6294416024725.9252120607
160.7606882412230.563965207884-0.12418143680.1371734795420.118639815260.4008063412350.2209713858920.2497707003310.0980924412513-0.570515465511-0.169699991893-0.1389404185680.350175303137-0.453518575531-0.0004965818635120.8430023794590.01873419935650.03776507155720.593638154857-0.03264973680120.5635382631217.1985005439-4.6994200524723.3213428049
170.3019809655850.19687274693-0.04810511128130.3203243748710.06341471683060.1405427717360.271287648782-0.0720910139449-0.4390223328481.32093738885-0.358885409392-0.7700104873991.64086558323-0.3915963803620.004886319591951.181531319750.0578874190036-0.1003078193910.712810429354-0.002452800179250.8960084504624.924638291-18.61845948827.6318129032
180.5100811838470.230380410660.234989758051-0.02570790908190.1780476270050.157063746791-0.4976593249660.107340974859-0.410867351160.1737790391340.278033680563-0.194594465811.35963735318-0.100022136280.0008651425183171.01066748408-0.05544756204610.01465866342210.650737789562-0.001794244581210.58392918180322.6018104935-13.107204227234.9167712361
190.362610566211-0.3812266549290.09197035252740.393270986915-0.03090438053060.07301333406230.5667946835530.860455788621-1.584808629540.813349401116-0.204606090126-1.842470066110.411679938778-0.2008935169260.006075931837311.411374708650.15964725705-0.04583404547861.049986465210.1030810290920.92405857603433.6470165935-13.659266307233.2570137033
200.0175995565236-0.101280606776-0.0658816804770.0410506061299-0.06316684279110.185608731714-0.698638595425-0.3576942371130.6424766661580.756975843920.289081485119-0.01161239301060.3165444492230.440281315953-0.009729611404970.509502132865-0.01074820220010.03519926004080.650926572936-0.09574565206220.67593685599519.2273859607-4.8216251315538.9147786988
210.4900388893560.4352233375020.3430118797920.2031987248880.3293651088070.2038943525420.229090282314-0.667516485640.1946484774920.0477499212821-0.163583868226-0.2461002009120.258021104278-0.0767944441831-9.14003379755E-50.9678451984750.06527430910930.0498959065890.688737645762-0.01840986204340.63986984384820.6979539447-3.618282788441.5739265666
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 111 through 124 )AE111 - 124109 - 122
22chain 'C' and (resid 259 through 267 )CI259 - 2671 - 9
33chain 'C' and (resid 268 through 291 )CI268 - 29110 - 33
44chain 'C' and (resid 292 through 318 )CI292 - 31834 - 60
55chain 'C' and (resid 319 through 348 )CI319 - 34861 - 90
66chain 'F' and (resid 268 through 328 )FK268 - 3281 - 61
77chain 'F' and (resid 329 through 348 )FK329 - 34862 - 81
88chain 'B' and (resid 1 through 13 )BA1 - 131 - 13
99chain 'B' and (resid 14 through 26 )BA14 - 2614 - 26
1010chain 'B' and (resid 27 through 56 )BA27 - 5627 - 56
1111chain 'B' and (resid 57 through 85 )BA57 - 8557 - 85
1212chain 'B' and (resid 86 through 99 )BA86 - 9986 - 99
1313chain 'B' and (resid 100 through 110 )BA100 - 110100 - 110
1414chain 'B' and (resid 111 through 129 )BA111 - 129111 - 129
1515chain 'A' and (resid 3 through 13 )AE3 - 131 - 11
1616chain 'A' and (resid 14 through 38 )AE14 - 3812 - 36
1717chain 'A' and (resid 39 through 49 )AE39 - 4937 - 47
1818chain 'A' and (resid 50 through 73 )AE50 - 7348 - 71
1919chain 'A' and (resid 74 through 79 )AE74 - 7972 - 77
2020chain 'A' and (resid 80 through 89 )AE80 - 8978 - 87
2121chain 'A' and (resid 90 through 110 )AE90 - 11088 - 108

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