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- PDB-6z0w: Crystal structure of the cytoplasmic domain of FlhB from Shewanel... -

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Basic information

Entry
Database: PDB / ID: 6z0w
TitleCrystal structure of the cytoplasmic domain of FlhB from Shewanella putrefaciens
ComponentsFlagellar biosynthetic protein FlhB
KeywordsPROTEIN TRANSPORT / T3SS / flagellum / motility / Shewanella
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / plasma membrane
Similarity search - Function
Flagellar biosynthetic protein FlhB / secretion proteins EscU / name from scop / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthetic protein FlhB
Similarity search - Component
Biological speciesShewanella putrefaciens CN-32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Front Microbiol / Year: 2020
Title: A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria.
Authors: Hook, J.C. / Blagotinsek, V. / Pane-Farre, J. / Mrusek, D. / Altegoer, F. / Dornes, A. / Schwan, M. / Schier, L. / Thormann, K.M. / Bange, G.
History
DepositionMay 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Flagellar biosynthetic protein FlhB
B: Flagellar biosynthetic protein FlhB
C: Flagellar biosynthetic protein FlhB
D: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)60,7664
Polymers60,7664
Non-polymers00
Water3,639202
1
A: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)15,1921
Polymers15,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)15,1921
Polymers15,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)15,1921
Polymers15,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)15,1921
Polymers15,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.436, 152.436, 126.886
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein
Flagellar biosynthetic protein FlhB


Mass: 15191.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: flhB, Sputcn32_2563 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y8K1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: XX

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976244 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976244 Å / Relative weight: 1
ReflectionResolution: 2.1→46.44 Å / Num. obs: 33095 / % possible obs: 99.96 % / Redundancy: 19.9 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1412 / Net I/σ(I): 13.46
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 1.233 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 3286 / CC1/2: 0.773

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0Z

3b0z


Resolution: 2.1→46.44 Å / SU ML: 0.2753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1852 5.6 %
Rwork0.2099 31233 -
obs0.212 33085 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 0 202 4134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114020
X-RAY DIFFRACTIONf_angle_d1.15985467
X-RAY DIFFRACTIONf_chiral_restr0.066623
X-RAY DIFFRACTIONf_plane_restr0.0075712
X-RAY DIFFRACTIONf_dihedral_angle_d7.6474542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.30381410.27432381X-RAY DIFFRACTION99.96
2.16-2.220.32851420.252389X-RAY DIFFRACTION99.96
2.22-2.290.29851410.23762362X-RAY DIFFRACTION99.96
2.29-2.370.29531400.24062378X-RAY DIFFRACTION100
2.37-2.470.27791420.24492380X-RAY DIFFRACTION99.96
2.47-2.580.32771420.23492405X-RAY DIFFRACTION99.96
2.58-2.720.27751420.24362403X-RAY DIFFRACTION99.96
2.72-2.890.30181410.23632384X-RAY DIFFRACTION100
2.89-3.110.24581430.23432396X-RAY DIFFRACTION100
3.11-3.420.28991420.21392406X-RAY DIFFRACTION100
3.42-3.920.22951430.1962412X-RAY DIFFRACTION99.96
3.92-4.930.20991450.16652429X-RAY DIFFRACTION100
4.94-46.440.20341480.20272508X-RAY DIFFRACTION99.89
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)
13.02471563593-1.55525640942-0.2280962696721.2533673798-0.1693581144572.192296274130.1694348110630.387340163764-0.170991099921-0.166503013341-0.04613970239140.1726444993660.106931854483-0.438124635051-0.1618349145560.3282300161410.0280987966314-0.02214762809720.336333682133-0.007496793506090.253641792169-10.7160745449-20.182491158814.314151861
22.60713092183-0.776727840439-2.857837695554.69599330896-0.4139605661355.984010693110.08172256071990.5842616869510.1328758236890.08512803143710.2716408261330.2753287677410.59941915226-0.817597194974-0.1992300307390.313188625235-0.0397659178267-0.03135556524530.3436518768-0.006052381323470.339023079956-8.3243056084-28.37948725128.4822289183
32.67381668213-0.589377976822-0.006037723083863.265387717171.498432364853.403113229350.2025301640550.294655350260.0638142630456-0.29391880807-0.1921740017330.155745391865-0.0200587982229-0.0249503972011-0.04329555634960.2880742484250.03351147122670.01133053119870.2684552706510.00213675367980.272781574515-4.93356440404-22.235042941115.6755372564
42.58761796080.118147299131-0.9844915243412.001971094241.145887659216.49788607290.00724380851657-0.5083139320371.001154032260.100220642837-0.0845135150897-0.240557687927-1.61538129784-0.0185941897888-0.1508368412120.5713044858140.06252775750710.0225513521440.519500314847-0.1226605599180.6375823116752.88061696692-10.833334158519.9955597246
50.918128084590.3950606269640.4039115850611.039139392270.4996473940690.396459872589-0.1575257447870.2348186406360.0203286739607-0.2187782967260.171869944187-0.0396186159175-0.0340080496010.090038685703-0.1421703318840.5333447661080.01549683735570.07307442094940.42170767598-0.02543247569040.4033025894025.18343881225-33.4523914956.75960214452
61.20662064701-0.304600120075-0.3164900566214.72461245704-0.4864270592812.24244143802-0.0878911612547-0.0630542621828-0.2763500475430.263736080939-0.0321987830295-0.2009953102980.326413057964-0.01801589977790.1843431177750.4270080193870.0491429294074-0.001399483519940.318106557796-0.0008123217893140.320954579369-19.3417905452-14.79207764948.4031163305
73.06379409640.8127432359412.825931846433.398678298654.298427322042.05059382283-0.257107276426-0.262782697459-0.2144090091850.3261923839790.502867058554-0.39436518637-0.7501314369921.1078693043-0.08863326515040.6227095965070.08207600036050.06520719945750.3812954155480.01324266646580.27660425573-21.2405098833-5.3021361322553.6743752034
84.16454611467-1.2660386506-0.3433957929071.730675395423.052070765916.619512245460.2422468190830.173702492233-0.3322128834340.179267485697-0.0460014014717-0.4362503366781.643296064230.0119444992378-0.2573172250230.494136590820.0703624138261-0.03790756505840.463871253904-0.02471786931480.342635355881-28.3020424042-8.7457572585335.8669960042
92.40593463002-0.783604949813-1.406804463942.141704783210.161108319624.25513008419-0.191742585594-0.5573538109040.02412002756451.06414752310.0266050068793-0.324980189093-0.1208246215690.4951590763650.1264277461740.7508432353020.0629963679876-0.1114181628650.2949036442970.03551077341750.363703707898-17.0693215669-10.669674371952.7806455541
103.09819433513-0.6469354571590.151206517671.94678432443-0.8732966383951.54456907982-0.306066951848-0.220306009589-0.4088611436580.8303785575390.2156553839710.33322592144-0.145709548332-0.4530851111020.0877925718460.4752037213180.09655477661980.1034714579790.353088091258-0.0168781135190.337484532795-25.1416563462-5.3221145953749.6727847028
118.0016090287-1.05483945539-1.493586146195.063590476151.032608804124.75039956042-0.540963456225-0.2678980808550.5932111321510.176330330660.4474267104570.0590615657536-0.365495679740.1690909936080.06760444491230.3588592489610.0125614368199-0.05103254889380.214400673925-0.003252704646770.262323604069-24.22688815722.2310905421740.9330916652
122.012873394010.39688205933.756359492420.4262846327931.062606856673.42447047714-0.967118828944-1.47347699969-2.163214688140.608262894550.251100886860.2930474762040.1909841496650.366256476010.144882379334-0.359148042734-0.5000129136830.1265688379720.5837467323070.2168160358783.57049523719-8.883302590370.058647205504840.6100120319
136.13419668537-0.1072653358362.202326902963.347396557420.2970148490373.23438975845-0.43083100013-0.206892893644-0.6135045836830.2597606522810.1426834817390.3848864262750.0138904134128-0.02357552007550.2379837475030.5800889939170.0139789004060.08620566369720.3721475900820.0240355375430.468698245279-24.61737429885.2473962187950.6742647597
143.29817497341-0.146561109260.4549078285812.824695613310.3473218213163.12137366638-0.0698737940611-0.291328415983-0.4762883557250.1719305076590.04515985985180.360669254502-0.0103862136957-0.6287333261210.01570720421390.3239219574570.01135002105740.03469751037880.3706260063540.03923855620850.385028532109-13.568806429-36.221470658345.3463547518
152.96334844102-1.550222939670.8979126785215.457591366692.200882816154.04284252156-0.0969743588481-1.45329246075-0.01013436853391.591922672270.064426349241-0.466599336882-0.492867890405-0.196726833961-0.163308632220.6422075176210.00393292980593-0.1372270989350.587142621235-0.1063666322630.398436236362-0.390737838526-31.623708975354.8632994528
162.62678787619-0.540611980365-0.9945323126455.21113029256-0.2001389197442.19667587797-0.1730018604780.492055369267-0.4343527657360.01998270637620.05881706512311.01399905657-0.0950465383233-0.4040025831720.2691808624130.328955423992-0.00248179426030.03825529913220.360629382826-0.02086072840820.478368950319-16.8913962231-35.339741864843.0068161209
172.08360385173-0.4246716448780.1426212785482.484036672030.4417409208022.164069515860.000132875895003-0.0489308580456-0.1331248953640.2668731391660.01202890253420.07812972651370.0485622017974-0.0170696577624-0.00552961507930.258048498416-0.00685144052530.0008813151200150.2096992377340.007207359921650.259815052225-3.44404204672-33.242602887641.5496851701
183.87475416330.280750143768-1.297434370351.841143142720.4094843966312.8080268303-0.265872532017-0.3929757265660.46035294643-0.235474270320.517146297123-0.539401376591-0.1340319658530.268508428196-0.1956156772820.2515524707070.0330285566685-0.05039058544110.391286030039-0.01943373209910.322043447464-0.0242356749421-23.494208321534.2138495703
195.848711965741.735757020981.041929180557.66710023236-0.2231271795185.731272253970.06806619358820.399416989305-0.838134317684-0.5434567415450.468696375126-0.423631767948-0.0281696951368-0.0996205122343-0.590497352910.5565036472140.07941332536290.03534563044060.304684226346-0.0251994454460.353837180722-0.696471635745-47.750654340334.8921404897
201.296773618580.3717043214871.052750583333.612334128543.282890206683.03291582778-0.2756550363810.3200222975010.153981545297-0.3440643001490.5631729297910.0284017177705-0.1257052199650.539931280953-0.1579350065910.371250199438-0.07189534729250.01157810510850.388813818022-0.05814373289750.361988133027-33.9791331069-15.738958207416.1368545945
217.086632159061.75724673245-3.00159482454.74695690718-1.003957645285.803146016620.4401507056010.447019604476-0.8528793408080.893096264612-0.6730067638050.235368120398-0.532979245819-0.4398525490950.1121442953080.428520319319-0.02669693044910.01242375118680.405531527868-0.09884934058010.374174004968-38.463127069-11.410401484724.9067355817
226.46131464306-2.03943155624-6.658118361530.6448583753562.115548140916.878689354361.920125242551.288654227960.498517791372-1.367213351370.0363152548194-0.764050534275-0.817403835742-0.402574399733-1.58236905891.015997292120.03125693417240.07342998417110.5554428523950.03448192530940.598753398162-31.0095209765-1.653219526928.71336326158
234.274894058660.4162235892360.5926682883413.245315985490.2211953051273.131891782520.132021754328-0.200725464103-0.6994225481160.2127322661010.02466703596080.35409844930.402762641387-0.0631271000025-0.240053637840.491349721302-0.0525191205595-0.04480543391190.345843131998-0.03257781569030.436422807742-35.6056362607-17.25046961721.813838175
242.57548919305-0.1993657861440.9448339489583.222100150280.3900121388651.003725319810.10280538131-0.24974542869-0.191387787809-0.315181380975-0.0262776961410.3460480713940.0951975635047-0.473320205079-0.04735795724710.329700482468-0.0351546781642-0.05569882496080.480510092115-0.04032616643570.487802043467-38.0114005811-7.200233031421.4582454054
255.96115886211-1.033272637991.752135737952.54031814371-0.1443046935572.111935204260.1226142955560.2036924829680.686115672737-0.121136760476-0.175327747301-0.3092985134610.1417356491850.008176480434410.0285446476080.36304777790.0010499250460.03520849268880.293832347987-0.0106055700670.311830960118-26.4483397985-0.95922246912423.6868208224
262.230643524780.175568548946-0.2253725506510.324012858502-0.09051808739030.0456887928763-0.101336618739-0.4647871317440.6021668624350.1709130834210.005065765182350.623015083148-0.3417065991450.2090624966140.1304427870550.4226377134770.05856628058690.03420289947120.311460392711-0.004031253674060.571743629658-12.2932238096-3.8351575099624.4195206834
272.41550559709-0.6606081120580.3034707366032.001702958260.1911674795162.5378406768-0.0004338500530540.07530850815620.359512133802-0.0232198079428-0.2441006818930.406526258850.0881806003723-0.6262190462310.1709567776780.3849036050140.0739447885992-0.04215560545910.550747626008-0.1102821724420.389047145125-34.79079179472.3360476054530.7620275306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 278 )
2X-RAY DIFFRACTION2chain 'A' and (resid 279 through 287 )
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 348 )
4X-RAY DIFFRACTION4chain 'A' and (resid 349 through 364 )
5X-RAY DIFFRACTION5chain 'A' and (resid 365 through 382 )
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 268 )
7X-RAY DIFFRACTION7chain 'B' and (resid 269 through 278 )
8X-RAY DIFFRACTION8chain 'B' and (resid 279 through 287 )
9X-RAY DIFFRACTION9chain 'B' and (resid 288 through 307 )
10X-RAY DIFFRACTION10chain 'B' and (resid 308 through 333 )
11X-RAY DIFFRACTION11chain 'B' and (resid 334 through 349 )
12X-RAY DIFFRACTION12chain 'B' and (resid 350 through 354 )
13X-RAY DIFFRACTION13chain 'B' and (resid 359 through 375 )
14X-RAY DIFFRACTION14chain 'C' and (resid 252 through 278 )
15X-RAY DIFFRACTION15chain 'C' and (resid 279 through 287 )
16X-RAY DIFFRACTION16chain 'C' and (resid 288 through 308 )
17X-RAY DIFFRACTION17chain 'C' and (resid 309 through 354 )
18X-RAY DIFFRACTION18chain 'C' and (resid 355 through 369 )
19X-RAY DIFFRACTION19chain 'C' and (resid 370 through 381 )
20X-RAY DIFFRACTION20chain 'D' and (resid 252 through 268 )
21X-RAY DIFFRACTION21chain 'D' and (resid 269 through 278 )
22X-RAY DIFFRACTION22chain 'D' and (resid 280 through 287 )
23X-RAY DIFFRACTION23chain 'D' and (resid 288 through 307 )
24X-RAY DIFFRACTION24chain 'D' and (resid 308 through 333 )
25X-RAY DIFFRACTION25chain 'D' and (resid 334 through 354 )
26X-RAY DIFFRACTION26chain 'D' and (resid 355 through 359 )
27X-RAY DIFFRACTION27chain 'D' and (resid 360 through 374 )

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