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- PDB-7ovp: Crystal structure of the chemotactic adaptor protein CheF -

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Basic information

Entry
Database: PDB / ID: 7ovp
TitleCrystal structure of the chemotactic adaptor protein CheF
ComponentsAdaptor protein CheF
KeywordsMETAL BINDING PROTEIN / archaellum / phosphorylation / motility
Function / homologyTaxis protein CheF1/F2 / Chemotaxis signal transduction system protein F from archaea / chemotaxis / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Taxis protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsAltegoer, F. / Weiland, P. / Grininger, M. / 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
DepositionJun 15, 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 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adaptor protein CheF
B: Adaptor protein CheF


Theoretical massNumber of molelcules
Total (without water)80,2962
Polymers80,2962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Mass photometry confirmed the sole presence of a homonymer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-44 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.620, 188.600, 58.290
Angle α, β, γ (deg.)90.000, 112.904, 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 Adaptor protein CheF


Mass: 40148.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58230
Has ligand of interestN
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 7.8, 0.1 M ammonium sulfate, 0.3 M sodium formate, 3% PGA-LM, 3% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→46.63 Å / Num. obs: 26066 / % possible obs: 99.92 % / Redundancy: 13.6 % / Biso Wilson estimate: 100.31 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.1
Reflection shellResolution: 2.75→2.84 Å / Mean I/σ(I) obs: 1.04 / Num. unique obs: 2567 / CC1/2: 0.563

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→46.63 Å / SU ML: 0.6227 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.5045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1113 5 %RANDOM
Rwork0.2373 21134 --
obs0.2398 22247 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.23 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 0 0 5544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565644
X-RAY DIFFRACTIONf_angle_d1.02147599
X-RAY DIFFRACTIONf_chiral_restr0.0557868
X-RAY DIFFRACTIONf_plane_restr0.0168945
X-RAY DIFFRACTIONf_dihedral_angle_d8.249733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.52941390.48052640X-RAY DIFFRACTION99.89
3.03-3.190.39831390.35882635X-RAY DIFFRACTION99.96
3.19-3.390.40021380.31722636X-RAY DIFFRACTION99.93
3.39-3.650.42611390.32612630X-RAY DIFFRACTION100
3.65-4.020.31471380.24662624X-RAY DIFFRACTION100
4.02-4.60.28361400.21162654X-RAY DIFFRACTION100
4.6-5.80.23091390.20812642X-RAY DIFFRACTION100
5.8-46.630.2191410.19252673X-RAY DIFFRACTION99.86
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)
14.95961776607-0.07974447402350.03664159412178.51047798807-1.518781083672.961859769620.311451175759-0.3617314579070.1145560481361.10945152999-1.06722267901-0.7626635430070.06503208475450.165774056281-0.1048927212420.675764106164-0.306591485994-0.07844852789830.536230267552-0.008170224096290.48543246804116.267144.0944.86
20.804243438326-0.7650690034860.8777710541340.6236106625-0.6369931955470.8261620595470.2987287762681.306695247110.382682855962-0.93431177638-0.0732143804921.681516845270.534612560959-2.02312286763-0.00389271278570.877021200341-0.129700252233-0.06461437138951.36509418829-0.0688659580771.14203560178-2.462155.54132.936
3-0.30251599743-1.1960441517-2.16751816817-1.234303173050.5165141398342.79189034219-0.2315326650580.287849871132-0.2131941493130.04503286106940.161605249639-0.1419609209650.270295065039-0.2695094457150.09883490645620.586847261183-0.162579562222-0.01206882389040.648446654474-0.1671671592850.5713017330780.452159.965.524
41.245936115410.2994309701380.7590593016231.332912594430.8506623597750.957662845810.605263116132-0.3758173716730.729211665243-0.206076210393-0.527049547465-0.862775573324-0.05964078684191.428801448410.1157271664590.7877823542110.0199738727990.06707935919440.9921846629550.2164573981160.81642627918140.161210.5114.867
55.424139637352.10094793388-2.964690989615.66969800002-4.9298563667510.4948909847-0.1575401973090.34513281315-0.29962939442-0.3086768505870.4581664023740.3088354721671.03747527415-1.376059885070.09459871172210.485957699836-0.113127350112-0.01918123789840.4408039104560.02694765137350.36926014147118.382199.831123.258
61.024733184460.2125131393520.4830970189371.132097672170.7971277950780.563424248818-0.03739020428540.3679559469150.0106427740874-0.2913584467660.309165063136-0.277124044993-0.1373353566970.2350995364470.015101405440.782045787928-0.174629783385-0.05834837041020.8443394463710.2628971347090.5809849405344.066182.8685.993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:168 )A2 - 168
2X-RAY DIFFRACTION2( CHAIN A AND RESID 169:193 )A169 - 193
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 194:340 OR RESID 341:341 ) )A194 - 340
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 194:340 OR RESID 341:341 ) )A341
5X-RAY DIFFRACTION4( CHAIN B AND RESID 2:53 )B2 - 53
6X-RAY DIFFRACTION5( CHAIN B AND RESID 54:246 )B54 - 246
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 247:340 OR RESID 341:341 ) )B247 - 340
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 247:340 OR RESID 341:341 ) )B341

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