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- PDB-8j56: Crystal structure of the FlhDC complex from Cupriavidus necator -

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Basic information

Entry
Database: PDB / ID: 8j56
TitleCrystal structure of the FlhDC complex from Cupriavidus necator
Components
  • Flagellar transcriptional regulator FlhC
  • Flagellar transcriptional regulator FlhD
KeywordsTRANSCRIPTION / FlhDC / flagellar master regulator / transcription factor / Cupriavidus necator
Function / homology
Function and homology information


regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / bacterial-type flagellum assembly / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Flagellar transcriptional activator FlhC / Flagellar transcriptional activator (FlhC) / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD superfamily / Flagellar transcriptional activator (FlhD)
Similarity search - Domain/homology
Flagellar transcriptional regulator FlhC / Flagellar transcriptional regulator FlhD
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCho, S.Y. / Oh, H.B. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Hexameric structure of the flagellar master regulator FlhDC from Cupriavidus necator and its interaction with flagellar promoter DNA.
Authors: Cho, S.Y. / Oh, H.B. / Yoon, S.I.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar transcriptional regulator FlhD
B: Flagellar transcriptional regulator FlhD
C: Flagellar transcriptional regulator FlhC
D: Flagellar transcriptional regulator FlhD
E: Flagellar transcriptional regulator FlhD
F: Flagellar transcriptional regulator FlhC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4228
Polymers94,2916
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-123 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.533, 124.533, 173.853
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERARGARG(chain 'A' and (resid 4 or (resid 5 and (name...AA4 - 1110 - 17
121VALVALGLNGLN(chain 'A' and (resid 4 or (resid 5 and (name...AA13 - 2219 - 28
131LEULEUPHEPHE(chain 'A' and (resid 4 or (resid 5 and (name...AA24 - 6730 - 73
211SERSERARGARG(chain 'D' and (resid 4 through 11 or resid 13...DD4 - 1110 - 17
221VALVALGLNGLN(chain 'D' and (resid 4 through 11 or resid 13...DD13 - 2219 - 28
231LEULEUPHEPHE(chain 'D' and (resid 4 through 11 or resid 13...DD24 - 6730 - 73
112SERSERGLNGLN(chain 'B' and (resid 3 through 11 or (resid 12...BB3 - 229 - 28
122LEULEUHISHIS(chain 'B' and (resid 3 through 11 or (resid 12...BB24 - 8030 - 86
132ASPASPPROPRO(chain 'B' and (resid 3 through 11 or (resid 12...BB86 - 10092 - 106
212SERSERGLNGLN(chain 'E' and ((resid 3 through 5 and (name N...EE3 - 229 - 28
222LEULEUHISHIS(chain 'E' and ((resid 3 through 5 and (name N...EE24 - 8030 - 86
232ASPASPPROPRO(chain 'E' and ((resid 3 through 5 and (name N...EE86 - 10092 - 106
113SERSERPROPRO(chain 'C' and (resid 23 through 79 or (resid 80...CC23 - 18023 - 180
213SERSERPROPRO(chain 'F' and (resid 23 through 71 or (resid 72...FF23 - 18023 - 180

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Flagellar transcriptional regulator FlhD


Mass: 12380.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: flhD, FHX61_004144 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7W4VD94
#2: Protein Flagellar transcriptional regulator FlhC


Mass: 22384.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: flhC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7T4G0G8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 4.13 Å3/Da / Density % sol: 70.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000, magnesium chloride

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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: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 20112 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.97 / Net I/σ(I): 9.8
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 989 / CC1/2: 0.358 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→29.91 Å / SU ML: 0.5178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8515
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2613 949 4.73 %
Rwork0.22 19123 -
obs0.2219 20072 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.22 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4863 0 0 0 4863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364938
X-RAY DIFFRACTIONf_angle_d0.57846716
X-RAY DIFFRACTIONf_chiral_restr0.0378821
X-RAY DIFFRACTIONf_plane_restr0.0038854
X-RAY DIFFRACTIONf_dihedral_angle_d16.5792956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.690.37391200.32332666X-RAY DIFFRACTION98.34
3.69-3.920.31761280.30112681X-RAY DIFFRACTION99.93
3.92-4.220.26631140.25322723X-RAY DIFFRACTION99.93
4.22-4.640.28211430.22152717X-RAY DIFFRACTION99.97
4.64-5.310.24931400.22726X-RAY DIFFRACTION100
5.31-6.680.2361550.21052744X-RAY DIFFRACTION100
6.68-29.910.2271490.17172866X-RAY DIFFRACTION99.7
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)
14.75070888949-3.46369026378-3.519926765723.268517772951.989373868617.971780814520.1855129658571.26643037059-0.70173772984-0.851813544822-0.2636922723351.124134554870.299909665537-1.549427131970.1388233829260.558823798217-0.0578947479984-0.1276105537950.7568500451120.1250518352160.7932549652780.9358162245113.5134577792.5083589508
22.39648509226-2.78068027727-1.339356563697.85238114825.532772246444.270845809750.137791462893-0.241629572171.7264110656-0.2119623929560.624683734695-1.83135444138-0.371880296554-1.0079894827-0.319005164430.8959591066420.208559583304-0.07917552307161.175813328630.02065297918530.13136321134880.8178286089128.1006657829.98317457376
36.23701814283-1.871928407731.596474043055.99234423226-0.6255863801892.57963151330.2133515948690.67712171953-1.50228522044-0.1743418851180.008635738797290.78898716545-0.3584577013520.03063569372420.07440193583090.6489238934180.003836310093630.2337463160040.434982659580.2199482512670.30176255323486.6416140492116.6343010150.632246465709
43.849816338960.07892486945991.554643336496.35254444188-0.4071625546960.4494973804040.216658248427-1.47479238663-3.02024461475-0.104060277410.1280980482511.74300096540.987150050639-0.293649206268-0.3309028577040.6616243938670.255636641246-0.001836709889910.880387173730.4401621868291.0796734057780.6230856947108.81719105111.0378139474
53.766950076031.479129602050.4761088168192.65430913117-1.999206399582.37538923172-0.55038600543-1.35221063603-2.20661326493-0.763106263288-0.119248741877-1.555956642311.004924649730.332522673906-0.06082469508320.729383429941-0.05541899525130.1635686684130.5785312151890.1790593625071.2712673237898.2164856252105.5207319076.87497681774
65.62747309485.01542444385-4.285649104014.47231397966-3.606978856515.105636959961.1358472296-1.6850251561-1.907817205851.04415251454-0.2163406734780.8932545744120.604115162683-1.25444731856-0.0963490392371.11452005816-0.1090588451350.06897573357581.414691695540.4928382445241.2650699674690.1053361986103.89082088618.1727742784
77.558285376481.550959118630.3094975595163.9907299857-0.958620043241.578991202170.067713240641-0.4260614652320.347504227898-0.427387151228-0.0905285918899-0.157794192997-0.1180006684230.098438354752-0.005646578105760.6861365596460.00236910535662-0.02104184947490.595719247615-0.036364877510.94774573070392.4409650429120.7872781961.89983506697
80.607920376394-0.503124613058-1.502603770543.564933643580.2027419912773.760537687850.572225844465-0.67051396357-0.6152356235980.7178250921030.1322140986290.6636471258670.3569858832280.0990626592073-0.566654488210.519139326516-0.1014838107330.1422462944220.878089776696-0.02025692016021.44537227579113.32862027388.7334349371-1.50935021144
97.00942385725.94802297024-1.958310033886.56685179045-2.910158063026.87829401041-0.2017243091890.03049840642980.616965832504-1.508482120710.309630511478-1.785236596650.6045785936990.8051197788930.03370188606830.542218651381-0.02951288329320.1915546401380.74854517069-0.2098925226911.25758874152116.59229380290.9150789802-11.0010572482
101.266837616610.82113745004-0.08440733437392.018980063810.4802201251010.07850668421260.012969797413-0.001189017497410.945569043672-0.8705294638-0.3502421513740.846226558742-0.0132720297058-0.3883846720980.5712369348560.71721332507-0.108685549107-0.1669989606360.911934684880.02030875349530.953355834977114.605952777105.053406348-16.6280612197
119.9389684757-0.03910698192672.746970175086.498539761-2.314347817154.40760643483-0.467606719329-0.02764969934570.47163541317-0.2213814061320.121429054298-0.249331103236-0.343075272129-0.2704960785830.3477575687220.573878142674-0.0599298672210.1621876711090.6220042476490.01026029714560.798020230969104.88162608108.938278217-2.57146209852
129.643395211612.2964845332-4.206324632343.291903371020.5226023441662.819249799370.08079968360680.18937167875-0.4887350163210.0704014978003-0.190801607447-0.456096466370.409184453980.568384301001-0.1610422279150.645035502339-0.123641116905-0.02960945952870.528162147648-0.09939554598360.839191295977111.658629415107.985579455-8.9756241671
135.304728567193.29758191208-4.094878620523.9604395131-2.183228102756.266784253760.794112879787-0.04019963150620.826747072244-0.395982864664-0.738239025184-0.16981479766-0.4563425228420.1382039184330.002448599314680.883148887121-0.07312853230490.1440410927650.700614458828-0.0286272473911.45778731305110.317934622124.803235047-5.5680846621
149.18280236961.42777689149-4.96139135227.80125895718-0.2610909480545.524162083370.578431273706-0.4042951991140.5403975398451.17739386429-0.452738373102-0.430213591768-0.750632214018-0.228650395447-0.3053193839410.694851156655-0.05702667772840.1167575847780.740264294749-0.1135243925810.74099715317776.665180037189.506476452525.936713379
153.775391512870.603607026693-1.482015707683.211931786710.8798667741787.45578694654-0.218276626461-0.3536729413980.5291930526870.242407385068-0.3587530369870.6104265396270.402861990872-1.469276083850.7462015451270.65652564963-0.1383189626990.07575968344460.796041892222-0.1175993952820.88838401182269.694879398983.469052244925.3064768271
165.316821012714.10008789179-1.983495517867.25285543194-3.192977918188.283321562810.871553917253-0.05073524336580.995039077592-0.09700587706940.05003397568070.823299197132-1.7349724375-0.776270653886-0.8732871500470.7267965076660.01219905508760.1369110790430.5810665692260.001018034493590.73159540618778.423499327691.442391666314.8322250656
175.48934867637-0.8275601952044.075707724522.32578505443-1.624072039784.74977666541-0.1555391572480.6371633984450.455843056646-2.30118851841-0.136083853332.24177669138-1.079222262431.035273667580.3602097911681.229478977910.0503795236853-0.3089704325680.8091402664360.1415437488560.90450679093876.304023928292.70297725635.58724573319
186.96284224068-2.79576895917-0.3962561917946.25780333549-0.3371667622314.44571850161-0.2187096841640.365059541136-0.5281860000170.489002420221-0.250728437057-0.07256552789510.144012087416-0.5488120366690.2729214369310.710567427743-0.1571589007420.115283840760.806686625549-0.06055298621940.92219377167474.765901565577.257598761922.2884631613
194.93701133592.879387977780.850544321545.86776290276-3.177563254583.29425897788-0.441428883237-0.03892507205680.273691803938-0.06530942920130.1423876694250.7025702031630.2268603657530.7808979756220.3096672082350.719780442020.02986479881220.05252435433060.711360519238-0.1292742007061.2825761262108.00300204377.93430675560.517950714327
206.632664896393.725253608733.622542682396.04463348449-0.6175674248464.102424595830.0505519551143-0.034513482265-1.043554443080.178384237869-0.184702217294-1.230939274850.3971987483660.8372537492450.1303838176630.7376814619560.03900433225870.1144729191770.664327818832-0.1750190163561.22113991087112.34113981670.94409008426.98334181927
210.521273166655-0.7173366577820.559886748451.00261493301-1.110354740831.48761960118-0.572084327267-0.127697805251-0.1810045174620.243692667037-0.0496307539716-0.53288548407-0.939234714748-0.2147954078670.3767411015830.9425752272990.0927517299895-0.1601140597930.839071944442-0.188118249660.961903967139105.28594221262.912686831616.9771440096
225.76156986409-2.13793391242.501477089087.77924955448-1.733271095534.62420457078-0.0608651837841-0.3158074361280.2218876523510.5060737055770.3183321122240.4067251631040.576656990267-1.83308281478-0.1452037384640.706674024552-0.04188039766870.1000210506590.665852877929-0.0703177095331.0231546989788.530147102768.38418252615.5931011723
236.02554609727-1.24870096255-0.7113771583217.637322785821.480301306666.05813265406-0.406947446562-0.2984028980360.8312036646450.194832505528-0.305239957810.0890033546857-0.254814287809-0.7423323698860.04958383610580.631043448083-0.1443147080710.05071752273840.598302795069-0.05835033322970.86095721394592.892744865876.036323182712.7504598843
243.6668023528-1.997336060913.327594460243.37384925316-3.819062907977.102096810420.240217947472-0.19176400841-0.8953247387720.793313780543-0.1419932321150.06870556023010.627507898543-0.1979370428540.0917271136030.791607856825-0.06062811976920.1353213993170.574967780228-0.1371488717231.0554984532497.366073865866.014353173414.2762763856
259.30353376984-2.20939922906-4.535103294897.98364616460.31591419236.278761374160.1938497364060.542752873082-0.527536006696-0.417759448349-0.387381154345-0.4232299268671.17387190695-0.5686623299130.3151476348150.843917723267-0.1249435421210.1922832287120.607059864738-0.2222178564511.3343479297183.442909521559.432302601316.015217994
267.082274501612.66660917467-2.212063005522.80377508654-0.329701707381.187340346550.1877828052780.00323223563695-0.789675350942-0.189647108981-0.897529268179-0.363952259990.397826296956-0.6218058740580.5165325968131.12157525611-0.03314418178450.2445560770420.76915207441-0.01685697958251.4508307811981.12372618756.731243289921.7439572297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 68 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 36 )
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 103 )
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 40 )
9X-RAY DIFFRACTION9chain 'C' and (resid 41 through 65 )
10X-RAY DIFFRACTION10chain 'C' and (resid 66 through 84 )
11X-RAY DIFFRACTION11chain 'C' and (resid 85 through 127 )
12X-RAY DIFFRACTION12chain 'C' and (resid 128 through 146 )
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 181 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 27 )
15X-RAY DIFFRACTION15chain 'D' and (resid 28 through 68 )
16X-RAY DIFFRACTION16chain 'E' and (resid 3 through 36 )
17X-RAY DIFFRACTION17chain 'E' and (resid 37 through 58 )
18X-RAY DIFFRACTION18chain 'E' and (resid 59 through 101 )
19X-RAY DIFFRACTION19chain 'F' and (resid 23 through 39 )
20X-RAY DIFFRACTION20chain 'F' and (resid 40 through 65 )
21X-RAY DIFFRACTION21chain 'F' and (resid 66 through 84 )
22X-RAY DIFFRACTION22chain 'F' and (resid 85 through 103 )
23X-RAY DIFFRACTION23chain 'F' and (resid 104 through 127 )
24X-RAY DIFFRACTION24chain 'F' and (resid 128 through 146 )
25X-RAY DIFFRACTION25chain 'F' and (resid 147 through 165 )
26X-RAY DIFFRACTION26chain 'F' and (resid 166 through 180 )

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