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- PDB-6lua: Cis-mutant R349A of the central AAA+ domain of the flagellar regu... -

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Basic information

Entry
Database: PDB / ID: 6lua
TitleCis-mutant R349A of the central AAA+ domain of the flagellar regulatory protein FlrC
ComponentsFlagellar regulatory protein C
KeywordsTRANSCRIPTION / Flagellar gene transcription protein / mutation / Vibrio cholerae
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 ...Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar regulatory protein C
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDasgupta, J. / Chakraborty, S.
Citation
Journal: To Be Published
Title: Oligomerization of flagellar regulatory protein FlrC is essential for cis-mediated ATP binding while c-di-GMP prefers its monomeric state
Authors: Dasgupta, J. / Chakraborty, S.
#1: Journal: J.Biol.Chem. / Year: 2015
Title: Unique ATPase site architecture triggers cis-mediated synchronized ATP binding in heptameric AAA+-ATPase domain of flagellar regulatory protein FlrC.
Authors: Dey, S. / Biswas, M. / Sen, U. / Dasgupta, J.
History
DepositionJan 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 regulatory protein C
B: Flagellar regulatory protein C
C: Flagellar regulatory protein C
D: Flagellar regulatory protein C
E: Flagellar regulatory protein C
F: Flagellar regulatory protein C
G: Flagellar regulatory protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,19414
Polymers210,7607
Non-polymers4347
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-9 kcal/mol
Surface area75920 Å2
Unit cell
Length a, b, c (Å)80.753, 154.633, 194.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Flagellar regulatory protein C


Mass: 30108.545 Da / Num. of mol.: 7 / Mutation: R349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: flrC, VC0395_A1719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AHP1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG6000, in 0.1M HEPES (pH 7.0) and 3% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→48.65 Å / Num. obs: 45041 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.076 / Net I/σ(I): 11.1
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 4337 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QHS
Resolution: 3.1→48.65 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.34
RfactorNum. reflection% reflection
Rfree0.2508 1998 4.45 %
Rwork0.1903 --
obs0.193 44941 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13438 0 28 33 13499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313740
X-RAY DIFFRACTIONf_angle_d0.57318573
X-RAY DIFFRACTIONf_dihedral_angle_d14.0515227
X-RAY DIFFRACTIONf_chiral_restr0.0232120
X-RAY DIFFRACTIONf_plane_restr0.0032413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17750.35741390.27142994X-RAY DIFFRACTION100
3.1775-3.26340.35811420.26783028X-RAY DIFFRACTION100
3.2634-3.35940.33971410.2553058X-RAY DIFFRACTION100
3.3594-3.46780.32061400.23522993X-RAY DIFFRACTION100
3.4678-3.59170.30761420.2343047X-RAY DIFFRACTION100
3.5917-3.73550.30721410.20573043X-RAY DIFFRACTION100
3.7355-3.90540.27711410.19573038X-RAY DIFFRACTION100
3.9054-4.11120.22931420.17873036X-RAY DIFFRACTION100
4.1112-4.36860.23211430.17183075X-RAY DIFFRACTION100
4.3686-4.70570.19461440.1453076X-RAY DIFFRACTION100
4.7057-5.17880.21241420.15863074X-RAY DIFFRACTION100
5.1788-5.9270.221450.17563107X-RAY DIFFRACTION100
5.927-7.46310.26091460.18493146X-RAY DIFFRACTION100
7.4631-48.650.15881500.14793228X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.68592.75963.18966.3583-1.56515.0003-0.28890.5534-0.3841-0.87640.44620.12390.42550.1764-0.12710.43690.04080.03660.2661-0.02690.260114.851261.9648-42.914
23.9737-1.44941.18963.2764-1.621.67360.0564-0.0305-0.00130.027-0.1099-0.01680.15650.0560.09790.22290.02450.05330.2652-0.03370.172828.345858.3593-27.8989
31.08190.64630.43813.35032.92493.3352-0.06940.24450.0316-0.30170.09290.00120.0980.167-0.11990.34240.0788-0.0090.31510.06390.239211.867748.9272-44.5978
43.2616-2.6898-4.55559.71091.75256.98380.10250.6573-0.7306-0.66210.00430.33660.4886-0.2035-0.23490.5623-0.0006-0.13470.4903-0.12210.32978.736533.8077-54.9516
53.18852.9169-0.8983.35271.31266.0697-0.21640.3296-0.08870.1830.3183-0.35120.7430.148-0.04460.40870.1172-0.09360.2598-0.05620.371415.112819.9724-45.0208
63.43190.07660.139-0.0850.18543.48540.1409-0.04650.02930.06350.0591-0.03020.25460.1242-0.17690.32540.05990.01420.1753-0.00760.270427.524329.5719-32.4238
70.3393-0.5999-0.03922.6337-0.19340.3545-0.0030.17150.0334-0.125-0.04180.05020.10230.10070.02990.2420.0297-0.0270.2901-0.04670.2612.0178.3094-36.3293
87.7254-6.3615-1.86798.1587-0.84916.8223-0.2454-0.0364-0.4197-0.3160.38870.05770.0239-0.0786-0.28110.3844-0.11390.04170.2135-0.10630.43288.9138-6.9091-30.4584
96.77286.2002-5.19087.605-6.50357.00840.1893-0.0252-0.2139-0.0325-0.40320.22820.45380.22870.14660.5385-0.09510.03490.205-0.08550.362312.7569-12.7402-13.9137
106.9738-1.4397-1.25565.42751.90152.9977-0.0556-0.2135-0.33330.54890.2916-0.5314-0.03330.4538-0.02120.2998-0.0729-0.1080.25930.00420.210717.1589-1.4289-12.7503
114.41970.46140.65260.10770.59572.77670.1296-0.3636-0.3299-0.0403-0.0707-0.00080.0363-0.0235-0.05960.24530.0371-0.05510.20080.04480.232229.69713.9702-8.9979
126.28681.3781-0.04047.50660.14143.84750.0464-0.11280.11660.1690.08080.28340.1291-0.2781-0.13030.23980.006-0.03210.2471-0.01490.158828.39359.3267-14.1941
137.49814.2793-0.14484.94861.93833.0838-0.3950.87410.0177-0.52150.5673-0.1221-0.5860.0418-0.11690.36120.00490.01410.30360.09080.149432.80568.0538-18.659
146.8737-0.62942.76997.3244-0.70263.3267-0.07030.6358-0.26620.431-0.24630.6612-0.4434-1.04660.15310.2433-0.0191-0.03920.34380.00170.252312.613611.666-17.2956
151.04040.49190.60190.5746-1.10566.47970.15650.1578-0.46570.0887-0.0453-0.1440.63910.3547-0.1190.43880.0108-0.03580.2153-0.01760.360411.3721-11.37224.193
167.3586-0.29082.43365.1362-2.17447.7324-0.4232-0.7439-0.2551-0.01170.10240.04970.9628-1.20130.13120.45430.0305-0.0130.45570.06180.31698.6741-13.961417.0868
179.8383-6.0118-0.26179.52145.77025.3933-0.07440.23360.47890.82410.3165-0.21840.1239-0.5341-0.13870.5011-0.01810.00850.26810.07070.273312.6209-4.068531.7262
182.85450.3055-0.98832.063-0.1590.0915-0.0115-0.23740.06140.179-0.1548-0.16130.0826-0.02330.16880.3343-0.058-0.10450.38320.01480.211828.58748.203521.2088
198.8845-1.38992.38292.586-1.30181.02720.00250.031-0.1427-0.1650.02470.05980.0977-0.09640.03750.2931-0.0165-0.02470.2622-0.07850.156222.83217.651610.661
205.64-4.8198-4.19689.25526.28494.52780.0069-0.10940.07961.03390.17810.29550.018-0.0998-0.32250.4367-0.04480.04540.29740.03380.33529.62582.974926.5069
212.84631.07850.5482.19621.17713.2076-0.0565-0.1915-0.1975-0.1670.1597-0.30190.2768-0.0712-0.14590.3141-0.0147-0.01040.24240.11340.219412.049512.742945.0135
226.397-2.1282.549.2093-2.73337.1809-0.6119-0.0532-0.299-0.38060.57150.45180.0129-0.08430.13770.41230.0534-0.00440.3988-0.02510.10978.836218.999151.2167
239.4964-6.0213-6.29443.82424.27577.65340.26910.01140.3110.8935-0.1024-0.4473-0.418-0.308-0.06040.4331-0.0175-0.02950.28050.01760.262912.859636.338853.1067
242.79610.0272-2.07740.7432-1.67523.46630.0832-0.18260.1402-0.0035-0.00220.1222-0.02310.3243-0.02930.282-0.079-0.02990.2211-0.06590.290328.509536.589436.6172
257.05570.62160.85140.7948-0.93362.0325-0.01650.0741-0.3755-0.0630.06210.0543-0.0438-0.1499-0.03530.3371-0.0095-0.03560.2216-0.06670.213622.772327.710130.8302
263.1256-3.20741.47693.4102-1.91872.0963-0.22140.25-0.0320.8313-0.26540.3827-0.0807-0.44440.24440.27210.019-0.03310.1954-0.0290.34399.405337.303244.2113
274.45231.780.24352.79691.67952.553-0.0764-0.2358-0.14720.03540.0377-0.12020.3058-0.0340.02350.2714-0.05640.03130.2225-0.04560.14111.953857.612648.1968
288.73765.63294.43837.66763.94465.8532-0.7830.46320.0583-0.9780.68330.3736-1.0989-0.32460.13190.40560.10050.05770.1057-0.01690.3368.969666.736947.3736
297.4016-6.79944.63819.2375-6.61729.69270.19840.49520.3671-0.7057-0.212-0.8128-0.6608-0.4243-0.05360.57490.07380.0160.2727-0.03830.326212.162279.205234.4055
308.7458-0.45147.99243.0987-0.31639.4820.5066-0.17390.2105-0.04240.0297-0.6362-0.4769-0.8766-0.31780.35350.01450.17130.28060.10470.1717.606769.345130.5985
313.568-1.5284-2.4452.64883.72466.28170.23620.0501-0.079-0.0707-0.081-0.3424-0.1378-0.1258-0.11430.2113-0.01310.00080.18470.04770.295328.444967.599624.4924
322.5269-2.4779-1.92294.30354.31124.50070.0210.0944-0.2386-0.33550.4467-0.3089-0.22370.2562-0.44760.3258-0.12010.00750.3446-0.05390.319734.782561.826322.1161
334.45071.5654-2.89167.98884.89427.28620.20310.20880.3727-0.0583-0.56530.30140.76140.40260.23950.1336-0.0136-0.00270.18340.04270.263223.517454.644126.0473
347.3471-2.6526-1.25263.03811.99044.3062-0.1685-0.38-0.50230.13850.15190.33560.48110.2671-0.05460.3384-0.06760.00010.12260.05570.265329.637258.596428.8773
358.42273.7043.86645.26934.43065.9499-0.0727-0.762-0.297-0.2501-0.0697-0.1687-0.2102-0.53860.09850.2523-0.00860.00710.30690.04620.247413.041554.375428.1504
360.35790.57180.43966.6485-4.06134.211-0.2308-0.0089-0.0354-0.0124-0.1079-0.4097-0.7661-0.07210.25320.56550.06610.00080.3713-0.01150.217211.035280.827724.6247
378.87870.54713.95943.4397-3.82257.24170.5168-0.12990.38550.2853-0.64540.16920.19841.7220.01910.5161-0.09150.03340.6404-0.04980.557720.278495.398714.4563
381.63892.0029-0.41793.3926-1.78162.6810.02930.04330.3542-0.2020.0697-0.16220.0689-0.0413-0.04120.55250.08050.10330.2216-0.040.2988.080186.289412.7468
392.97574.79610.11467.9548-0.84927.8738-0.26930.29381.0159-0.6299-0.03540.6024-1.361-0.19090.29450.64780.11610.0230.2256-0.01580.60128.736393.46377.653
403.4574-1.8549-0.08412.4590.4764-0.08420.14290.08130.0937-0.1805-0.1267-0.148-0.1146-0.0294-0.01060.3515-0.0290.04620.31610.02020.155526.475476.1897-3.4576
410.35220.1679-0.05270.2855-0.74515.041-0.0146-0.04380.09150.09230.10180.17230.0242-0.3947-0.07660.23510.07540.070.29920.02050.24411.532278.7442-20.3364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 130 through 165 )
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 361 )
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 376 )
5X-RAY DIFFRACTION5chain 'B' and (resid 130 through 165 )
6X-RAY DIFFRACTION6chain 'B' and (resid 166 through 285 )
7X-RAY DIFFRACTION7chain 'B' and (resid 286 through 361 )
8X-RAY DIFFRACTION8chain 'B' and (resid 362 through 376 )
9X-RAY DIFFRACTION9chain 'C' and (resid 131 through 150 )
10X-RAY DIFFRACTION10chain 'C' and (resid 151 through 165 )
11X-RAY DIFFRACTION11chain 'C' and (resid 166 through 211 )
12X-RAY DIFFRACTION12chain 'C' and (resid 212 through 249 )
13X-RAY DIFFRACTION13chain 'C' and (resid 250 through 271 )
14X-RAY DIFFRACTION14chain 'C' and (resid 272 through 292 )
15X-RAY DIFFRACTION15chain 'C' and (resid 293 through 361 )
16X-RAY DIFFRACTION16chain 'C' and (resid 362 through 376 )
17X-RAY DIFFRACTION17chain 'D' and (resid 131 through 149 )
18X-RAY DIFFRACTION18chain 'D' and (resid 150 through 230 )
19X-RAY DIFFRACTION19chain 'D' and (resid 231 through 292 )
20X-RAY DIFFRACTION20chain 'D' and (resid 293 through 305 )
21X-RAY DIFFRACTION21chain 'D' and (resid 306 through 361 )
22X-RAY DIFFRACTION22chain 'D' and (resid 362 through 376 )
23X-RAY DIFFRACTION23chain 'E' and (resid 131 through 150 )
24X-RAY DIFFRACTION24chain 'E' and (resid 151 through 230 )
25X-RAY DIFFRACTION25chain 'E' and (resid 231 through 292 )
26X-RAY DIFFRACTION26chain 'E' and (resid 293 through 305 )
27X-RAY DIFFRACTION27chain 'E' and (resid 306 through 361 )
28X-RAY DIFFRACTION28chain 'E' and (resid 362 through 376 )
29X-RAY DIFFRACTION29chain 'F' and (resid 131 through 149 )
30X-RAY DIFFRACTION30chain 'F' and (resid 150 through 164 )
31X-RAY DIFFRACTION31chain 'F' and (resid 165 through 205 )
32X-RAY DIFFRACTION32chain 'F' and (resid 206 through 230 )
33X-RAY DIFFRACTION33chain 'F' and (resid 231 through 249 )
34X-RAY DIFFRACTION34chain 'F' and (resid 250 through 274 )
35X-RAY DIFFRACTION35chain 'F' and (resid 275 through 292 )
36X-RAY DIFFRACTION36chain 'F' and (resid 293 through 319 )
37X-RAY DIFFRACTION37chain 'F' and (resid 320 through 332 )
38X-RAY DIFFRACTION38chain 'F' and (resid 333 through 361 )
39X-RAY DIFFRACTION39chain 'F' and (resid 362 through 376 )
40X-RAY DIFFRACTION40chain 'G' and (resid 131 through 271 )
41X-RAY DIFFRACTION41chain 'G' and (resid 272 through 376 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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