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- PDB-6xrr: Structure of SciW bound to the Rhs1 Transmembrane Domain from Sal... -

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Basic information

Entry
Database: PDB / ID: 6xrr
TitleStructure of SciW bound to the Rhs1 Transmembrane Domain from Salmonella typhimurium
Components
  • Putative cytoplasmic proteinCytoplasm
  • RHS repeat protein
KeywordsCHAPERONE / SciW / Rhs1 / Salmonella / Type VI secretion / T6SS
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Bacterial toxin 47 / Bacterial toxin 47 / Inner membrane lipoprotein DcrB/EagT6 / DcrB / RHS protein / RHS protein / Mog1/PsbP, alpha/beta/alpha sandwich / RHS repeat / RHS Repeat / PAAR motif ...Bacterial toxin 47 / Bacterial toxin 47 / Inner membrane lipoprotein DcrB/EagT6 / DcrB / RHS protein / RHS protein / Mog1/PsbP, alpha/beta/alpha sandwich / RHS repeat / RHS Repeat / PAAR motif / PAAR motif / YD repeat / Rhs repeat-associated core / Quinoprotein amine dehydrogenase, beta chain-like
Similarity search - Domain/homology
RHS repeat protein / RHS repeat protein / Putative cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSachar, K. / Ahmad, S. / Whitney, J.C. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: Elife / Year: 2020
Title: Structural basis for effector transmembrane domain recognition by type VI secretion system chaperones.
Authors: Ahmad, S. / Tsang, K.K. / Sachar, K. / Quentin, D. / Tashin, T.M. / Bullen, N.P. / Raunser, S. / McArthur, A.G. / Prehna, G. / Whitney, J.C.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Putative cytoplasmic protein
I: Putative cytoplasmic protein
J: RHS repeat protein
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: RHS repeat protein
D: Putative cytoplasmic protein
F: Putative cytoplasmic protein
G: RHS repeat protein
H: Putative cytoplasmic protein
K: Putative cytoplasmic protein
L: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,87124
Polymers160,71812
Non-polymers1,15312
Water20,1411118
1
E: Putative cytoplasmic protein
I: Putative cytoplasmic protein
J: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4686
Polymers40,1803
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-101 kcal/mol
Surface area15610 Å2
MethodPISA
2
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7569
Polymers40,1803
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-120 kcal/mol
Surface area15950 Å2
MethodPISA
3
D: Putative cytoplasmic protein
F: Putative cytoplasmic protein
G: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2764
Polymers40,1803
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-55 kcal/mol
Surface area15670 Å2
MethodPISA
4
H: Putative cytoplasmic protein
K: Putative cytoplasmic protein
L: RHS repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3725
Polymers40,1803
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-80 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.306, 105.306, 248.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein
Putative cytoplasmic protein / Cytoplasm


Mass: 16611.746 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM0290 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7CR57
#2: Protein
RHS repeat protein


Mass: 6956.042 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: D8W49_24030, DVZ53_24005 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5X2E0H7, UniProt: A0A0F7J3Q3*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25mg/mL protein, 0.2M Ammonium sulfate, 0.1M Bis-TRIS pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.9→91.2 Å / Num. obs: 126623 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 30.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 12473 / CC1/2: 0.539 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SciW

Resolution: 1.9→91.2 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 6333 5 %
Rwork0.1864 120272 -
obs0.1877 126605 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.85 Å2
Refinement stepCycle: LAST / Resolution: 1.9→91.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 60 1119 11645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004510772
X-RAY DIFFRACTIONf_angle_d0.679914612
X-RAY DIFFRACTIONf_chiral_restr0.04531620
X-RAY DIFFRACTIONf_plane_restr0.0041907
X-RAY DIFFRACTIONf_dihedral_angle_d16.40273960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.34192080.32983880X-RAY DIFFRACTION97.89
1.92-1.940.34362100.30233980X-RAY DIFFRACTION99.98
1.94-1.970.27562050.2733927X-RAY DIFFRACTION99.98
1.97-1.990.27422080.25843995X-RAY DIFFRACTION100
1.99-2.020.2652110.24923946X-RAY DIFFRACTION100
2.02-2.040.2862080.24853965X-RAY DIFFRACTION100
2.04-2.070.27382120.2434019X-RAY DIFFRACTION100
2.07-2.10.2472080.23293947X-RAY DIFFRACTION100
2.1-2.140.24132080.21663952X-RAY DIFFRACTION100
2.14-2.170.24012080.21083995X-RAY DIFFRACTION100
2.17-2.210.2482100.21373961X-RAY DIFFRACTION100
2.21-2.250.24762060.213993X-RAY DIFFRACTION100
2.25-2.290.2272120.20863978X-RAY DIFFRACTION100
2.29-2.340.24512130.19784016X-RAY DIFFRACTION100
2.34-2.390.22512100.20573968X-RAY DIFFRACTION100
2.39-2.450.25272060.20963984X-RAY DIFFRACTION100
2.45-2.510.24032120.20254004X-RAY DIFFRACTION100
2.51-2.580.22432120.19723977X-RAY DIFFRACTION100
2.58-2.650.23362080.1993998X-RAY DIFFRACTION100
2.65-2.740.23192120.20123981X-RAY DIFFRACTION100
2.74-2.840.21762090.19064028X-RAY DIFFRACTION100
2.84-2.950.2242120.1884007X-RAY DIFFRACTION100
2.95-3.080.2052150.194040X-RAY DIFFRACTION100
3.08-3.250.22532100.18624015X-RAY DIFFRACTION100
3.25-3.450.20132130.16824038X-RAY DIFFRACTION100
3.45-3.710.18572120.15414041X-RAY DIFFRACTION100
3.72-4.090.18532140.15884082X-RAY DIFFRACTION100
4.09-4.680.1592150.13454091X-RAY DIFFRACTION100
4.68-5.90.16692180.14964142X-RAY DIFFRACTION100
5.9-91.20.21922280.24322X-RAY DIFFRACTION99.78
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)
13.38504378581-2.208386767330.1123129761896.966471319074.277417217877.98088620140.07570643516420.4186242208580.569167212402-0.3067675110.105025307939-0.994917524581-0.6220475462850.693643171523-0.1927672438890.29965446435-0.06196426718690.007428843318430.327829040460.1259281306130.424854878-14.95223032524.8990485181-60.8300559399
22.1561623383-0.522973440790.9476438753621.66262708167-1.192854774872.598781846890.07762221417670.160254986245-0.0345471648541-0.0146058870392-0.0590347575597-0.006346271424260.03805951455220.02125040541680.0003306622804010.2579419729950.02750103154480.0178335516110.184381581498-0.005825867741030.196032077487-35.530825699327.1553367289-70.4079978839
35.102000119810.8977938065871.780767861592.903033560761.963175526086.141024656910.1448144418170.0182587477982-0.2382330691690.248532055462-0.191113638166-0.04373751351730.183942154323-0.0853102163150.1518144236860.2786916549850.06453202874510.001934130130680.1954409269190.03511082929290.196446020706-38.712698509830.0036073285-70.3811836598
42.82959544021.03014126367-2.379781225041.460106209820.0328685017573.015280948410.13184054720.150834866922-0.0149361694383-0.0226431272348-0.1284339349070.0287520590395-0.0228657708895-0.0331502095301-0.007660879945980.266387235450.03261531106360.001396542811270.1850273310720.04745919344050.216364511162-36.04750296429.0622799378-68.0279265547
58.88789758499-1.79031101646-0.9990279133062.257398109430.3691366990032.43144543325-0.0518079189289-0.2211827221920.446483589040.06226106582890.083557956624-0.0925037932452-0.1010751825690.100289892740.04218505299750.3308438723370.0203200944722-0.01593220021710.1535962132060.01313022458270.203284842501-36.757486288236.7068148128-61.1094065999
64.52005004157-3.28349869818-3.766684087338.599379470823.040999167324.26094395955-0.332098337293-0.7461835286470.3093203899180.5630728762840.3635876496650.397960749526-0.5186852524230.0718043946576-0.05577308842440.4104838821460.0654479651335-0.03820645405360.3505901395830.02666527507310.276963772461-27.75641547434.1230978758-54.6827561904
76.17762704961-2.64006554016-1.606562217194.45516720415-0.1228186751044.79618738187-0.09565152491840.388255245986-0.083705560724-0.0639705773474-0.07105622361670.01468374325080.0354394403109-0.2196519812820.2371601642910.185023085881-0.0247557117125-0.02555425042830.175833312952-0.0003135077972880.201400743571-24.292091498217.9508357069-59.0276739419
83.514453855850.202843593580.9041993668443.849235868950.646139814154.79766863198-0.0548395432773-0.101618086487-0.4584194895860.6476615061940.1137436287760.489878242750.332074661825-0.252742868559-0.05181928217990.3335260169260.04810087226480.06728532539020.1581707134620.06545582437040.383953708589-25.21559402524.00929816821-47.9889323219
92.88228283630.2824586948970.7163039760075.964301029190.998533978943.77111619373-0.05586097337770.14543613713-0.265672912290.03074917709860.125127806799-0.413608796632-0.0937942594180.262568966207-0.07537657116950.1662386044440.0418552306239-0.01235726524320.1720561527520.01559033785830.25431906169-15.411327757910.7167225819-53.7228392744
102.88165068842.0771658781-2.814062623833.35475363576-3.581605091834.28303310280.458959201578-0.7731064204961.2524812720.9215776450870.234106210299-0.276210986686-1.055748261410.261181976527-0.8927907602270.541971697762-0.0534947569632-0.06650275902890.367966744229-0.06350237545230.606592178644-14.324023015126.4392980998-48.0443085395
114.73746764299-4.808620534422.837962982055.55365297878-5.032499450778.43706621884-0.0138601773403-0.310027856639-1.6175413951-0.7300640551270.2612249747490.8553604471720.933332421282-0.826885620459-0.2640323466920.449033407401-0.03255486817620.02009617286380.3216629527090.02606419757220.49434019352-39.94551852716.0714855626-56.7087253452
122.92232098111-2.42198631932-1.706231145653.771256127941.559133833342.050324685060.1403267272520.284345579557-0.327388753468-0.151398297864-0.02768419142020.245765638635-0.232679251549-0.328820283011-0.2157900761980.237516209320.0256077171004-0.004787266371370.244059043143-0.009658261714550.313141739347-25.63945791279.80027258403-59.1970247433
138.09440627117-5.56188678247-2.110938348723.952233843871.244993657161.27349754572-0.1190435721620.575554251346-0.140472841684-0.5045722442240.0961142749686-0.1351369862390.201777054726-0.493754915971-0.08515572924430.4776537328210.0511263026345-0.1250533623280.425128178213-0.09671476902060.45613643105-27.451745654712.1945631606-71.1088670206
143.957744654354.41780390444-1.656885478989.99836852397-4.274819591714.956339806950.131547778170.047922866636-0.6203830040260.0410972190724-0.251041188157-0.4328062285670.400893969654-0.06937303449790.05406112053340.363957912375-0.00558744767362-0.01878496895730.261815247428-0.06062943441410.308876326306-33.479659536218.6403463358-67.9288504457
152.261282736551.50692604115-2.239025977642.06112241651-1.727407462432.30595728529-0.6168386968670.804206668295-0.188201551961-0.925033871155-0.176454556399-0.863130187510.484378152279-0.6342561307660.9502297720870.713817429196-0.00724226394169-0.1100869491050.633517750589-0.1204756076770.649409312494-34.74286330477.22504849841-63.1531870652
168.3415129628-1.46327241383.680046700134.281114404971.477946646422.8012486836-0.2655058867832.26164667070.789353924533-1.78324221413-0.2571045860590.1137056267360.06043909384040.581778451430.898935595440.859610614443-0.2800474138330.006854979189650.7356573311860.04162806772640.46947765972519.575990917312.9565212197-77.7347599992
176.08968336204-0.1969429831180.7033402022215.07078390469-0.2567798882011.789178926370.02599856185050.354765176620.0237181755038-0.299320854854-0.131494743466-0.2421749676390.131183756468-0.08445974201570.1234185042210.490929506857-0.201211197290.08186498403680.3273799550180.01641092796410.25138447518622.638842227514.8680870668-68.1103000168
183.51995548128-0.185765602197-1.218767544413.212390861111.435377508992.47554966635-0.0157643959767-0.0347809473039-0.1207900911710.4064239066460.02935077186110.2309428795060.420579550514-0.201080860641-0.04969508473170.28137550364-0.0729231381212-0.01995598064280.1739304886140.0005516577703820.22699848043332.106818604529.4049285733-65.1474595376
192.25407656966-0.0681052040897-0.8872555582632.829465778311.200260673062.20768438143-0.130004246153-0.0832010435825-0.07751852887120.1909228065920.0222679201980.1098841636890.422578803816-0.06363207217240.05275548806780.308231300633-0.0775365021193-0.004212478692740.1848146045540.03386227882990.25275529024638.207394140827.2450496268-63.5448088916
205.93411213632.603689484313.368087637244.864172449063.259288701042.82254196718-0.07928214838610.0290272765322-0.7359724039160.0004364381802430.174946781973-0.3342524786910.271731606555-0.0952433614702-0.08547291743170.387905098422-0.06564934237650.05231716005690.2287304474330.03162961799950.35352733868543.635777098417.7506501486-64.2852277401
213.896422159913.456107982823.952158743673.773600584543.975041960924.4710979371-0.2153408552670.5263579083580.0343810743545-0.403789721265-0.0118549311360.1887387922050.08942729025490.3863375017010.2808654926840.3476795349340.0299771730248-0.02548410410270.2873097798-0.01397640445410.3411711589324.0337572364420.8224437188-33.0595562188
223.111845268011.027726783891.837468900827.833438925296.322700907398.7354132764-0.206169316496-0.1113437186550.250932129356-0.01227076346510.04677380804580.199970734018-0.275876073497-0.03933327214120.1397641848120.2323664418950.002784148984280.01133557772330.1395328724750.0383797102760.277175453990.066454961107228.7163644534-23.3175553809
232.15940890235-0.4889371088230.3740877843833.25381642734-0.4938901379721.515336983750.02026704616350.015614858038-0.0296596841825-0.02964692271470.01431126536430.307532357334-0.155648302078-0.215127878766-0.03855547272720.2012397097770.0368725538934-0.003001873669440.148014250949-0.0173847723920.23395998412-6.833678175142.9258918462-23.8401009236
243.18432464292-0.783781082132-0.692027971784.042119228572.003582956268.172074125-0.0412806885872-0.07157626065360.01869667107890.0682819396238-0.04746008493570.1270124717220.0319011811451-0.09721759651210.05313752851060.1903933348220.0151594198168-0.02605354049290.0930991782407-0.0006298169562190.230335214714-2.4016195522942.9852959862-21.6352800166
254.087973907620.249174974993-0.1742463519186.73068922984.539250301648.512338878130.08020865753130.152676864582-0.07591039000720.04579225182870.0513685321485-0.5355869554830.09889644715810.0396048990271-0.2349638278340.21606812134-0.0155647087536-0.003391057940190.1574073472740.02770548388210.2747010641778.2739319721343.1999338216-22.4629951148
266.701887047931.91967621776-1.181204980738.54858506628-0.5505304019477.753027503650.3342879366760.475392855235-0.402933515143-0.5559945343120.154013780097-1.241444210540.922158855943-0.233276581616-0.6911548354650.510216398323-0.2379573421480.08282668620290.322746256476-0.05566255261520.4639594739633.65077306189.55601031371-68.9392336541
272.959638847390.204107306850.8581587486980.662294520775-0.5907820146954.581485361060.0845780796383-0.1648627629030.2958358665690.0898397419563-0.0985284740389-0.2836522147150.0567015699506-0.101622294966-0.2173751419660.555725697908-0.2047723961140.01870644879380.301396686294-0.009339464031370.35307446392824.481334996816.2335188088-63.0982342028
285.42563502935-2.845819148633.32008141097.22265643853-3.868370606434.6423290712-0.378914010084-0.4460782694840.501688750040.697138295430.219401216762-0.376011010106-0.700671599272-0.393251940390.1559725980170.610539226326-0.2288333496040.05201920840690.355847301144-0.02672958335020.30698938135616.733089567414.5909642944-59.5619607771
292.464638469920.668559003350.2012904614682.72942761278-0.6528775728381.738487438330.164009773458-0.2503270201730.09563698316710.340438234755-0.104426689080.1763243894650.036567377881-0.201691306137-0.06410902103970.584158749204-0.2515959756390.06918125474760.377814683265-0.02190075236550.31594878003910.48063000919.56298757443-57.4006503277
309.5785667659-0.7582897103279.150319004553.58735836842-4.088538686622.006349960910.9078970981741.08486588032-1.91457504883-1.28032397431-0.028681938345-2.298921102991.979172148610.666163401554-0.437416621451.32165388066-0.2476674357540.2032977855220.289777546897-0.07004217108260.79044495949822.63288391470.0436878001183-71.2899545872
317.77633436567-6.042350654892.79705599834.75391753137-2.679490230145.01805011704-0.0651019676330.09617267452140.8612856339961.10350447786-0.215531511758-0.644598927637-0.5311425301050.180555647410.2204834895240.662500921138-0.2321649863490.01938041316080.427755528932-0.05162318578580.46278005308516.052097555219.1804565921-55.1470475783
324.12025062515-5.08506267646-1.058003543236.389717970482.328054026428.00941513069-0.6687918975410.6457932933091.004436282141.60625222539-0.6828867214051.193446495-0.923859224333-0.5724428664881.230526794420.901833100147-0.2988625764660.05612822142340.651186804262-0.08339999199361.0719493364519.911509218830.0069658499-60.1676056649
335.425433475715.40150855967-4.285362847068.86207636706-2.833447090054.10763935266-0.454337232741-0.161812846587-0.1135303631050.5028308355220.281483132544-0.2246688661390.724398787795-0.1921278138730.3059487587760.457227905844-0.0514690134145-0.002107138496890.241639616128-0.02512343066460.32886334067629.114362762828.2002553585-62.6515483761
343.947763639714.05461413235-0.4745479218925.54851339558-2.286165791242.426986991440.385004048373-0.4197376444040.287511297704-0.421035379030.0003002978946651.05590574590.407056699319-0.974499728385-0.09747424732481.29068537933-0.252618231049-0.08542628455990.46815705925-0.1041914677420.5920985204224.105630026724.6081029168-54.5878802563
353.57084810027-1.873408290082.994891907972.17699809536-0.5897915189993.326685473210.811274754373-1.067706941620.240354839018-0.4853235446430.7835371735820.348239469373-0.4660651988-0.105217791091-1.03248543451.01363026571-0.2359571318130.010522453360.645875991754-0.2160494384540.98447331747419.491985594925.6001854379-48.6485910477
362.118959700770.6197596475171.027515892999.91854860087-1.603356946889.13444208572-0.1446243466310.5976023746260.269172219575-0.295399259260.141023352923-2.60077367126-0.9806140074222.32538280357-0.07205298613550.634337607575-0.13193406843-0.0273586972220.926070396558-0.03977664679530.7913715207315.769089638474.2270080119-62.2837348045
374.14926562821-1.981705106851.33027584146.930412141981.223730792065.372892513790.0824518723034-0.1257674598570.1297436991490.510458302947-0.068253965793-0.62557964646-0.2918830030560.362403348353-0.002418678799920.423839504067-0.116384521044-0.04836066154530.3492829052410.006620603880130.1732791746885.54872793769.5343449964-62.0734184474
380.980737264970.815193432434-0.2957978464642.479296962670.07076423097382.437220539710.0161613902475-0.0628920505019-0.06538283464060.221253006522-0.0606686082748-0.1190224402720.1107546910650.1552295813880.04356806497110.2364145539420.0152698302547-0.03678236904440.328695328180.002813046041150.175664240422.2758448491259.6194103396-78.1192827558
395.800767309560.7257830318060.2725332767783.57810105184-0.1195361267153.46466308968-0.0464618513109-0.169147671649-0.04832307887730.221559833943-0.04489997579690.1016380703780.066054329240.01845304791440.1080401892880.2708490033920.0388877919723-0.0229984913670.276718720548-0.02962095357860.155396639976-3.1278300696561.3686944327-76.4286507877
409.62673657064.717586987391.516174346716.992337933930.7216693659443.65761499575-0.0504301360979-0.2808945295310.1388577254010.0579641342037-0.04794332213520.0764017237655-0.46591906045-0.1966159681690.1289238959410.3539759243680.05394660777630.002452594583170.300987426718-0.01981987784520.167707884164-7.087819302271.7040803103-77.4192908261
413.694374598943.644149250742.678204762874.188406659683.008608762542.746137223610.258965957091-0.0130221894051-0.2591297417470.2671264359880.161172479425-0.6442358686480.08322864430510.462790303952-0.4233793111970.2913409712840.0380388538444-0.02381398744130.286305006336-0.008199693636870.38446254548910.750854265732.0284297542-25.8132324452
423.686187314281.045797906033.28362362374.083771190341.029887357218.17643434783-0.0593744043377-0.08424641109650.122528651770.09104990928080.06844910523650.282664359499-0.138705269081-0.2583371891510.01892269069990.2285545276630.05257344887730.03764722925190.136533438921-0.01735157538670.310578911408-2.0031594018323.167779005-21.7633205029
432.52684352716-0.333689115393-0.2088408044093.075958898250.2745065130253.06079366550.0381143891824-0.182091216374-0.2258677320980.473396186541-0.08514216772570.2011008281270.351964640945-0.08747024467310.02803066618040.3903844277080.00455059333050.01602990298810.1435510706250.01350480184830.310030529145-1.5780586242110.0344579714-13.8487805623
442.488895094641.90293675241.779804267241.725727204110.9508503981792.197997687390.0878393107413-0.04221175513250.1388708807210.189513123858-0.05058139716640.203455224730.290089409752-0.03549015274120.02033418849550.3312359084550.0107205387611-0.02174050769550.157040434786-0.00675737636040.362056878518-2.2366566222913.7523106298-19.7966509845
453.834875755654.35485006934-2.112330271655.41802995627-1.135141780372.36769446359-0.1059285772240.4439920356110.166075464624-0.1536362130140.2630707061210.1641511227610.2258351495-0.174785638103-0.07335017361080.323921644560.00368617760039-0.03688686557290.155293031839-0.0222138073110.292272478036-2.6784520956410.0826852059-29.7356985561
463.63092084687-0.8765442566472.810175704423.612956900173.15274047996.534358863840.090973546909-0.912358092136-0.5710924648851.941462929980.8666447399930.3590263030090.554691049751-1.12171432559-0.7428885559320.590508935239-0.003401890060670.03141061848220.4594884027530.1198361450750.528240729711-1.4597347096533.5785805757-6.92119672051
473.16051075412-0.5132798356411.035486423784.68469358274-0.3467760573132.33268343022-0.0318488576608-0.0587905661097-0.1172325043870.484243419329-0.05158662374020.6807916362760.27843419402-0.1589543666090.09535219237590.280033222853-0.004594169926150.0650245582650.171991332964-0.01001796288920.384026418643-7.2059141980520.8013485013-15.4552596817
486.07668400913.93608648628-0.5042664405747.82440346774-1.425561656591.4300008612-0.365097569209-0.0273653510869-0.481965673472-0.08281048914070.3119405028040.947045364680.159176973844-0.2237417870840.09453918626570.2897106041460.03038197803310.04877738549840.263113846671-0.02334684971240.501216233886-11.100383041332.2031614227-20.6059593465
492.04551218182-0.1893288834411.001476963932.33788407797-4.615152242459.50055228165-0.28451718362-0.358098948058-1.55510574206-0.7437749132380.2855804312110.2944810911811.05761676438-0.0444477033432-0.02885605854510.4553162583380.02484128211790.1492943083910.45790899446-0.05819452054190.697300382963-10.625967443728.2375255614-13.1772248488
503.884150372940.1643546634592.524080006828.8834421104-2.30820895928.742946857570.05364392512151.1039035871-0.0341491771445-0.366010938291-0.395894949808-0.4529562110070.710392769683-0.2577160813660.5450045151820.8099201856240.1099319215950.1339933266360.781216410862-0.08208079117230.89567456503-13.447709778625.5186013931-9.01081253165
514.51116862211-4.31825783883.597731186564.55239848049-3.440041485043.02989749776-0.1767858920590.7289965844750.548524798678-1.015395022740.1200793152931.21415389134-1.50926423906-0.1117764437810.07124626468140.9034138706990.0572082844082-0.1852315305310.661810128881-0.07244070197850.575373559873-4.4466110893479.7169953587-67.5633351041
521.434473422962.48285434846-0.8064900457425.16840253114-0.5873198695037.51889929010.0767392930001-0.1926104905040.4777685924270.208180391721-0.1727335195430.342647796714-0.666522016855-0.4957169553120.05866905212940.3828546895740.00578551214521-0.04159195657460.360353259154-0.06129408631850.247869336908-0.97125204125572.2802544358-64.6680656309
534.56553182321-0.3972300205250.3675707500794.22636537761-0.2356915846254.93397135206-0.0085060655973-0.311414987415-0.2640394276361.18370022421-0.09072667298420.2737878539690.42952103816-0.6060730771850.08339308003030.788805945414-0.152426475650.01508179576790.570421525572-0.06524847644650.254083075525-0.75090984016463.000334869-48.4065488925
542.207700178432.40104608522-1.617766817785.44633920155-0.5411491433921.72867757277-0.177755671685-0.7597656923420.03267451432021.08222511772-0.186376339461-0.358273225975-0.0343590681725-0.1456204938970.234659046511.04496881227-0.127668188223-0.1058675849640.740739479908-0.08915577350750.334697139234.2564769373866.8091237749-37.6162311019
553.442520028671.323308571870.3673029612943.927014539630.5857328340614.99817978641-0.0346410198236-0.3611111818270.04610442119511.16779792772-0.0400565866099-0.739229919889-0.05973372207870.08931583453220.07268925459480.621359940625-0.0505494094814-0.1758069199010.481075904539-0.01676864383360.2696354331067.6319858052268.4541678061-47.5894327509
564.98821190644-3.126713868922.514144318997.4148532277-6.91748477866.46974120523-0.03509630258761.87494722234-1.42696834574-0.5710219986271.048459867511.10048114873-0.236307881752-1.67490137333-0.8000787892511.00541437906-0.06934300845660.03021456577331.45388067821-0.1424625420430.670842217502-12.014311213862.61001944-60.5256377071
576.33630619347-3.0122007214-3.852032734297.11557732260.2221651751953.645354731680.755902867197-0.11312514299-0.3973433300680.314408140298-0.4001797673460.09199380036930.61713071797-0.798448577459-0.1694714875420.798052474786-0.206790702161-0.03914100346520.588501238437-0.03137713852940.320211881129-1.9432475158962.7409018362-51.126286352
585.57728523709-3.62505145502-4.387720478914.589377343753.21671047368.536229246150.7364228530410.511026248476-0.0810897394692-0.265576687004-0.7892872140120.1038068734230.789095106475-0.4964610094830.1871020971921.06106948502-0.119962003658-0.02686703738210.6744971182010.0438929143370.5312779465095.2388252133253.7224076792-55.3620610864
597.059483930660.639141985148-3.745295136491.83825226257-2.116836035116.48483405828-0.06393187983890.29425460724-0.615721023751.1556690751-0.288759101088-0.5063144228251.07132812413-0.3055138551930.130029880811.644759329280.133566709274-0.1793020013360.711168526288-0.1493234776230.6155664847115.4034853205652.8219006187-64.1993473899
608.156238137280.987886624954-3.72775150789.19614114604-6.988256351117.688420019450.475457162229-1.27061614512-0.2826764678221.3689196948-0.2284007453950.751428302870.3077905703690.168252361523-0.1935040393830.792396134283-0.141642498903-0.008690305172590.579593945741-0.04096970482240.430876156221-1.7812924018255.5934811595-63.767771168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:21)
2X-RAY DIFFRACTION2(chain A and resid 22:82)
3X-RAY DIFFRACTION3(chain A and resid 83:100)
4X-RAY DIFFRACTION4(chain A and resid 101:126)
5X-RAY DIFFRACTION5(chain A and resid 127:146)
6X-RAY DIFFRACTION6(chain B and resid 1:14)
7X-RAY DIFFRACTION7(chain B and resid 15:46)
8X-RAY DIFFRACTION8(chain B and resid 47:76)
9X-RAY DIFFRACTION9(chain B and resid 77:138)
10X-RAY DIFFRACTION10(chain B and resid 139:147)
11X-RAY DIFFRACTION11(chain C and resid 8:17)
12X-RAY DIFFRACTION12(chain C and resid 18:30)
13X-RAY DIFFRACTION13(chain C and resid 31:40)
14X-RAY DIFFRACTION14(chain C and resid 41:51)
15X-RAY DIFFRACTION15(chain C and resid 52:57)
16X-RAY DIFFRACTION16(chain D and resid 1:6)
17X-RAY DIFFRACTION17(chain D and resid 7:28)
18X-RAY DIFFRACTION18(chain D and resid 29:64)
19X-RAY DIFFRACTION19(chain D and resid 65:125)
20X-RAY DIFFRACTION20(chain D and resid 126:145)
21X-RAY DIFFRACTION21(chain E and resid 1:14)
22X-RAY DIFFRACTION22(chain E and resid 15:31)
23X-RAY DIFFRACTION23(chain E and resid 32:82)
24X-RAY DIFFRACTION24(chain E and resid 83:126)
25X-RAY DIFFRACTION25(chain E and resid 127:146)
26X-RAY DIFFRACTION26(chain F and resid 2:13)
27X-RAY DIFFRACTION27(chain F and resid 14:32)
28X-RAY DIFFRACTION28(chain F and resid 33:46)
29X-RAY DIFFRACTION29(chain F and resid 47:142)
30X-RAY DIFFRACTION30(chain F and resid 143:146)
31X-RAY DIFFRACTION31(chain G and resid 16:32)
32X-RAY DIFFRACTION32(chain G and resid 33:40)
33X-RAY DIFFRACTION33(chain G and resid 41:46)
34X-RAY DIFFRACTION34(chain G and resid 47:52)
35X-RAY DIFFRACTION35(chain G and resid 53:56)
36X-RAY DIFFRACTION36(chain H and resid 1:6)
37X-RAY DIFFRACTION37(chain H and resid 7:34)
38X-RAY DIFFRACTION38(chain H and resid 35:85)
39X-RAY DIFFRACTION39(chain H and resid 86:124)
40X-RAY DIFFRACTION40(chain H and resid 125:146)
41X-RAY DIFFRACTION41(chain I and resid 2:14)
42X-RAY DIFFRACTION42(chain I and resid 15:46)
43X-RAY DIFFRACTION43(chain I and resid 47:99)
44X-RAY DIFFRACTION44(chain I and resid 100:124)
45X-RAY DIFFRACTION45(chain I and resid 125:145)
46X-RAY DIFFRACTION46(chain J and resid 8:13)
47X-RAY DIFFRACTION47(chain J and resid 14:32)
48X-RAY DIFFRACTION48(chain J and resid 33:49)
49X-RAY DIFFRACTION49(chain J and resid 50:53)
50X-RAY DIFFRACTION50(chain J and resid 54:57)
51X-RAY DIFFRACTION51(chain K and resid 1:6)
52X-RAY DIFFRACTION52(chain K and resid 7:27)
53X-RAY DIFFRACTION53(chain K and resid 28:70)
54X-RAY DIFFRACTION54(chain K and resid 71:77)
55X-RAY DIFFRACTION55(chain K and resid 78:146)
56X-RAY DIFFRACTION56(chain L and resid 11:17)
57X-RAY DIFFRACTION57(chain L and resid 18:24)
58X-RAY DIFFRACTION58(chain L and resid 25:34)
59X-RAY DIFFRACTION59(chain L and resid 35:38)
60X-RAY DIFFRACTION60(chain L and resid 39:56)

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  • 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

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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

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