[English] 日本語
Yorodumi
- PDB-6z0w: Crystal structure of the cytoplasmic domain of FlhB from Shewanel... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyFlagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane / Flagellar biosynthetic protein FlhB
Function and homology information
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: XX

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more