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- PDB-9egd: AclA from Tenacibaculum discolor in complex with intermediate for... -

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Basic information

Entry
Database: PDB / ID: 9egd
TitleAclA from Tenacibaculum discolor in complex with intermediate formed by C8-Lysine attack on ADP
ComponentsTHIF-type NAD/FAD binding fold domain-containing protein
KeywordsTRANSFERASE / N-acyl-cyclolysine / biosynthesis / signaling
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine dehydratase / cyclic threonylcarbamoyladenosine biosynthetic process / ubiquitin-like modifier activating enzyme activity
Similarity search - Function
ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme
Similarity search - Domain/homology
: / ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / THIF-type NAD/FAD binding fold domain-containing protein
Similarity search - Component
Biological speciesTenacibaculum discolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsShirkey, J.D. / Jeffrey, P.D. / Linares-Otoya, L. / Khatri Chhetri, B. / Donia, M.S. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI172144 United States
CitationJournal: To Be Published
Title: Discovery and characterization of a widespread chemical signaling pathway in environmental and host-associated Bacteroidetes
Authors: Linares-Otoya, L. / Shirkey, J.D. / Khatri Chhetri, B. / Mira, A. / Biswas, A. / Neff, S.L. / Linares-Otoya, M.V. / Chen, Y. / Campos-Florian, J.V. / Ganoza-Yupanqui, M.L. / Jeffrey, P.D. / ...Authors: Linares-Otoya, L. / Shirkey, J.D. / Khatri Chhetri, B. / Mira, A. / Biswas, A. / Neff, S.L. / Linares-Otoya, M.V. / Chen, Y. / Campos-Florian, J.V. / Ganoza-Yupanqui, M.L. / Jeffrey, P.D. / Hughson, F.M. / Donia, M.S.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIF-type NAD/FAD binding fold domain-containing protein
B: THIF-type NAD/FAD binding fold domain-containing protein
C: THIF-type NAD/FAD binding fold domain-containing protein
D: THIF-type NAD/FAD binding fold domain-containing protein
E: THIF-type NAD/FAD binding fold domain-containing protein
F: THIF-type NAD/FAD binding fold domain-containing protein
G: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,05024
Polymers210,3947
Non-polymers4,65617
Water00
1
A: THIF-type NAD/FAD binding fold domain-containing protein
B: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5648
Polymers60,1132
Non-polymers1,4516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-30 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: THIF-type NAD/FAD binding fold domain-containing protein
D: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3526
Polymers60,1132
Non-polymers1,2394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-29 kcal/mol
Surface area19750 Å2
MethodPISA
3
E: THIF-type NAD/FAD binding fold domain-containing protein
F: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3526
Polymers60,1132
Non-polymers1,2394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-30 kcal/mol
Surface area19970 Å2
MethodPISA
4
G: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules

G: THIF-type NAD/FAD binding fold domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5648
Polymers60,1132
Non-polymers1,4516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9000 Å2
ΔGint-32 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.122, 83.875, 162.948
Angle α, β, γ (deg.)90.000, 105.491, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLU(chain 'A' and (resid 2 through 250 or resid 301 through 302))AA2 - 24916 - 263
12AMPAMPA1BIHA1BIH(chain 'A' and (resid 2 through 250 or resid 301 through 302))AH - I301 - 302
21LYSLYSGLUGLU(chain 'B' and (resid 2 through 249 or (resid 250...BB2 - 24916 - 263
22AMPAMPA1BIHA1BIH(chain 'B' and (resid 2 through 249 or (resid 250...BJ - K301 - 302
31LYSLYSGLUGLU(chain 'C' and (resid 2 through 249 or (resid 250...CC2 - 24916 - 263
32AMPAMPA1BIHA1BIH(chain 'C' and (resid 2 through 249 or (resid 250...CN - O301 - 302
41LYSLYSGLUGLU(chain 'D' and (resid 2 through 250 or resid 301 through 302))DD2 - 24916 - 263
42AMPAMPA1BIHA1BIH(chain 'D' and (resid 2 through 250 or resid 301 through 302))DP - Q301 - 302
51LYSLYSGLUGLU(chain 'E' and (resid 2 through 249 or (resid 250...EE2 - 24916 - 263
52AMPAMPA1BIHA1BIH(chain 'E' and (resid 2 through 249 or (resid 250...ER - S301 - 302
61LYSLYSGLUGLU(chain 'F' and (resid 2 through 249 or (resid 250...FF2 - 24916 - 263
62AMPAMPA1BIHA1BIH(chain 'F' and (resid 2 through 249 or (resid 250...FT - U301 - 302
71LYSLYSGLUGLU(chain 'G' and (resid 2 through 249 or (resid 250...GG2 - 24916 - 263
72AMPAMPA1BIHA1BIH(chain 'G' and (resid 2 through 249 or (resid 250...GV - W301 - 302

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Components

#1: Protein
THIF-type NAD/FAD binding fold domain-containing protein


Mass: 30056.287 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tenacibaculum discolor (bacteria) / Gene: CSC81_02270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G1BYE5
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-A1BIH / N~2~-octanoyl-L-lysine


Mass: 272.384 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H28N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
Has ligand of interestY
Has protein modificationN

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.0, DL-Malic Acid, PEG-3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.15→29.62 Å / Num. obs: 45960 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.134 / Rrim(I) all: 0.268 / Χ2: 0.98 / Net I/σ(I): 5.3
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 4 % / Rmerge(I) obs: 1.536 / Num. unique obs: 4488 / CC1/2: 0.541 / Rpim(I) all: 0.867 / Rrim(I) all: 1.767 / Χ2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→29.62 Å / SU ML: 0.4709 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.0731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 2354 5.13 %
Rwork0.1935 43551 -
obs0.1964 45905 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.97 Å2
Refinement stepCycle: LAST / Resolution: 3.15→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13987 0 308 0 14295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008214606
X-RAY DIFFRACTIONf_angle_d1.272719699
X-RAY DIFFRACTIONf_chiral_restr0.07242145
X-RAY DIFFRACTIONf_plane_restr0.00772493
X-RAY DIFFRACTIONf_dihedral_angle_d23.29385500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.210.41541280.3682522X-RAY DIFFRACTION98.88
3.21-3.280.34571310.31642553X-RAY DIFFRACTION99.44
3.28-3.360.37531360.30442551X-RAY DIFFRACTION99.04
3.36-3.440.36921450.2832547X-RAY DIFFRACTION99.3
3.44-3.540.32621370.28432529X-RAY DIFFRACTION99.22
3.54-3.640.29831480.25562530X-RAY DIFFRACTION99.33
3.64-3.760.3191310.22062540X-RAY DIFFRACTION99.11
3.76-3.890.26651350.21872548X-RAY DIFFRACTION99.22
3.89-4.050.2751320.20422550X-RAY DIFFRACTION99.3
4.05-4.230.2431350.17622586X-RAY DIFFRACTION99.52
4.23-4.450.22771500.15152541X-RAY DIFFRACTION99.34
4.45-4.730.18071430.1422533X-RAY DIFFRACTION98.75
4.73-5.10.19671430.15422572X-RAY DIFFRACTION99.23
5.1-5.610.25031450.16482579X-RAY DIFFRACTION99.49
5.61-6.410.20821280.1692602X-RAY DIFFRACTION99.71
6.41-8.050.21131490.16772599X-RAY DIFFRACTION99.82
8.05-29.620.19011380.14692669X-RAY DIFFRACTION99.4
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)
10.3669879550191.08281872042-1.471724583149.25715932453-7.109941280417.18691783873-0.188097927229-0.1270213304051.310272694161.78577935568-0.4104487227950.205989924601-0.670913027666-0.9683105605180.7337537414340.7397186493020.237154163297-0.07010470833430.608771500005-0.2265387139871.21069972832-59.33139773418.072889508262.822530767
23.276152738761.53504278091.166182733253.547751895551.001100002364.70558819015-0.308067872169-0.1302791087791.344774168090.3029689180590.055117309656-0.0596773530526-0.4579568454210.02707723774750.1601658660130.8112439581950.0127513740632-0.3611337120660.335416254005-0.04898242973061.06449283184-41.706341190623.05471101161.6902190021
30.3330657910920.4037409991090.2632149514011.64220175648-0.04476027449240.684640193736-0.459134406625-0.1282048210980.5913325895070.218298375242-0.248015787844-0.0241691699749-0.660018964186-0.178523485437-0.1134594299841.10332990016-0.0268634034417-0.6338978202850.314533831118-0.06855108273461.41946248022-36.984206102930.681441852359.4152460004
40.005017768085810.0707410386830.02918866525211.126758589320.5025460799140.2205759516670.606392738787-0.7057420242850.636277782340.408171988451-0.1828539310470.0166355770815-0.4991413845470.3324458761830.9318794268790.953242811429-0.288914525507-0.489434426210.382117642815-0.3713666602330.853023986103-32.69929433121.566376074372.3498313156
50.976632613942-0.3362670612330.3628901115553.049933773781.214094938252.341431551740.144369588243-0.3648487004960.07170544175860.6216465434630.103773590884-0.809501029099-0.1186272221910.1214613892960.203823121880.79526221002-0.0323341877852-0.4342240032650.154282672055-0.05829507072040.978586520981-29.52783006313.983010519163.6945156155
62.72096055631-0.1619102128431.232809649766.653574065342.439311128732.60549790905-0.1120637774070.1450999941660.0230825497811-0.0101107555993-0.19701190068-1.037312228560.2880928884170.847292617947-0.0878265146660.6934192245340.0221048933232-0.2421704907430.4723401436280.02695053778930.921167018898-24.11338864414.7858560397659.5801562128
73.17145892745-1.62680743363-1.528868019163.50493294401-0.4131119721586.556234053380.2639841478690.3032460676940.502326186338-0.136278659544-0.133841020058-0.4063243035240.3012463964960.672939637929-0.194135666240.611016321449-0.0700728814534-0.4444679036280.514969289198-0.05318694890140.902763472261-32.41080576989.5937370338650.4025912192
85.08762135532-4.914602261330.3065835475157.50380960201-2.627223993526.766839760360.095430884586-0.173172474267-0.1886991676920.520569110557-0.1379193103750.03302012627590.823445321066-0.493231536323-0.1103187023560.653994706343-0.124491765801-0.3562481051660.2894079403970.01468388148830.687727718903-39.27042699953.7508542022660.4509786692
92.58515673026-4.81096486535-4.039861870949.391174465398.236799373187.45122402508-1.01201237716-0.06115965116970.760300251527-1.577048806920.0685097570822-0.358324886713-2.283591115021.586806557720.4752926733570.871102549423-0.330207981384-0.5373166564820.9564521305610.2462962409831.54152042316-30.484829968820.257640242339.2953563895
101.97922158654-0.9973161585430.4817458328073.247686325120.6320276660433.12163298407-0.6280986117760.3280208788770.994052015569-0.575039662596-0.2212383496050.468254030492-0.946129422441-0.2091959510690.5329945179770.8628665674940.00746177178788-0.4842626581210.5450943114950.06638445611721.21087772785-51.993536827424.782990814140.262745833
112.424788907060.110837908004-0.4269666960092.24022090065-2.136328836057.61348410309-0.04752991585760.6614729328080.109475343891-0.1027052929060.07712096942260.601902713135-0.386177660945-0.216320277837-0.07476593582050.7448656546160.0653426085189-0.4862954051640.4720336620160.07710113478541.09020976158-57.958605564811.846875403837.3245115246
121.59782776429-0.1424398019771.750869067742.292331968780.5005198670917.25180177238-0.1932311713660.126269604163-0.283450439772-0.219589741557-0.4325116133830.690145226421-0.403818499651-0.699242290207-0.0253296758370.6639622902690.0675459484685-0.2780150121520.557451942935-0.2124493473151.01776641519-61.954555890.22230534489243.2031154411
131.35420773816-1.91766951887-0.278737408795.073323415933.537894201087.87548653821-0.194811842694-0.0339525728614-0.5008459517580.993934234266-0.2383804805241.296449775430.535748757195-0.8397060931730.7039421604110.685175201327-0.118822592625-0.1760055837850.522098847849-0.08570576993231.04385411796-62.11712626575.2939953387658.2817810902
145.260726243992.62986192633-3.074087422071.33372931025-1.625310725869.26868694424-0.05240729674120.349747433509-0.072720856790.0039244338329-0.134045284375-0.343483784821-0.3426170804650.1513112026360.3450805055750.5042856402540.0225347430758-0.1913870210540.3949711319020.05773149088660.922585738744-45.55393611212.612287417943.8266941965
158.224001494954.46053909832-1.198612282274.037203521852.066889390875.57074299374-0.1380763106860.654074631307-0.89270147068-0.179813267425-0.0786293441272-0.3504558408241.145940012760.05817114799460.1888984687720.5911897352360.0901293866165-0.3362841650880.376706381678-0.1120471097961.0103454192-47.10467414762.8132717589541.9608990459
169.785171059880.7857956746390.1774893770773.25614805695-4.677682456486.91489252308-0.405091072364-0.5024930671181.658138346390.8404076966850.297083261341-0.752676965147-1.26044134546-0.18246500449-0.04827187665740.6931321887630.126789849229-0.2569488655440.690177657395-0.1978675967641.4259058357-4.8442490160559.018011611924.8086760196
174.28720089206-1.22139324579-0.9351321352936.22254349329-0.6201123025012.875964276710.0352359964847-0.2537626368150.784860735985-0.2521427563620.2975480596570.833850153086-0.255490004065-1.006097079150.01670839075650.3025803235880.1040107688720.05818136372590.988007490244-0.08167865572010.551741290319-15.736338681346.630560438425.9224235403
182.79355584217-1.94575282136-1.594441960053.51276045671.129610808282.37563297866-0.192576307922-0.4934472743620.4497248675160.1521506691310.138092077191.16979159992-0.586428637535-0.786718006295-0.1458248150540.3282222573010.1387588420980.04888224814081.10762384613-0.1294542153620.780775436001-19.401174957347.244781690931.0578489982
192.852079215650.403734413953-2.553050316346.24612497333-2.437275104393.57214319168-0.6023590363530.83897944920.241997434704-0.4506032736750.38094552274-0.1972515155290.0271023865775-1.216785790730.1606026162910.4556346758670.169397003246-0.1150503594761.16271587648-0.004646128909341.10929538885-23.832222719847.545167702713.2666555861
205.080734969550.4651009920241.01023483242.311088788480.70500418571.285716405470.1607472457210.6436427493240.391837852952-0.582872235296-0.08640584103180.5420445887530.0104601007629-0.723060241057-0.1029808104630.4111675947260.217886679714-0.1649831140490.835475313594-0.08389462564910.744257999143-13.554689481944.216963483910.548218388
216.011092239992.81421676236-0.8919406952436.10647483148-3.037658850446.440823873830.826773177150.869177970034-0.7519822590390.167620129787-0.7055549658180.6895648154320.0960692348846-0.928872154005-0.1258430581780.373499066703-0.113310363708-0.04919463144031.455843073040.06689950316171.03828274624-14.752629769937.92309172752.11564879837
226.66119493182-0.0707319686634-3.130129373877.09974497939-2.004639253412.95373623591-0.5621678624651.23649654125-1.04662478205-0.5927448910850.35591886980.07046640288351.02925856304-0.5413524501440.1247699300690.447630622785-0.1629134080920.002947555556970.826674692058-0.08322029217740.528944761021-6.9081393495126.771031043512.5616044784
238.298918789311.595181025-2.941121014166.06566761202-1.787084859315.68448872304-0.01199431261750.7145128703440.4597915224920.2032330984660.0347644743874-0.369319409832-0.3815130684160.416461511359-0.06324996197530.2410180108980.063159605472-0.1164391588860.567663023469-0.1408674438190.59442192673-2.6032353013845.264411554915.814973326
247.993659453590.263310844804-1.239487029137.136264763456.52528418657.89987213581-0.920141730614-0.802273336594-1.342690677570.626552089590.3039433301271.408729073231.0523612327-0.514220930390.6018551817210.739270893578-0.0253767683620.02048452049981.061295291640.1855180964171.13605243923-13.386848508825.484759334929.1520138502
254.223270215461.112648066530.7171843781965.94991096381.333922621284.3997684175-0.134689195347-1.091200682390.702327094680.331086433391-0.398089514004-0.20528625935-0.483613197314-0.2510892636210.4081178307030.3577631801960.0876951915007-0.03079559208921.01069251502-0.1036404409120.587053887483-4.0519007411539.985903038239.779372547
268.783322398455.195665342961.31673823883.473862936331.488148093533.927788229970.462300875917-1.773549451060.1740607596691.37246965537-0.1859277170660.4927513202540.241408432206-0.469131537314-0.1443520045850.5967486216250.140184246874-0.02909729768051.4393760618-0.08908803423050.67994831637-9.0034333109438.930984259145.0994409492
276.409779623172.250209891231.343386670312.749766622213.146343779664.320958823840.129419178012-2.29218408780.4967708286211.748139799010.229532795045-0.8697304949320.8034627764710.666267009757-0.4738724880011.00102016190.206777143882-0.2022250620861.72735988586-0.05514531217730.7310969176798.5970764176939.3114332852.8041660612
282.4336061537-0.817184184325-0.4022662823838.68824559641-4.042677000287.349642054220.43687459549-1.82095635770.1548197852521.917289238210.151771137937-0.8796806456540.0179146550590.759256223009-0.4452567271010.6095928232640.112366164797-0.1401131842111.1317581668-0.1063404845740.6222604601379.2932375478938.612702765643.4127789399
294.4231458544-2.872569050381.93498092587.29304560609-5.015659101975.50735450234-0.136454723931-1.434515196030.5518441648330.705375578601-0.955413212997-1.71155330684-0.1795451690982.083544435220.7607890303810.8303867508290.151104188708-0.4732927412941.707633022510.02086431994251.3200549677515.491867814234.629429954145.0133230595
306.649916458750.8686090164730.6167396821934.44625282285-5.28020434699.025331765710.4728173804780.07476813558110.390834256966-0.230141133049-0.921625097852-0.3339553834920.5609788853541.486960850280.3597068819750.4531892065240.183377027828-0.2603812453420.922110877662-0.1021017252520.8663823402259.0217862647538.986030276932.2088419786
317.82908110477-0.63642328954.000941943498.999862906723.181548923755.35007728986-0.95441502067-0.5970725011380.9620189329220.1879899842460.8404969265661.03672819345-0.357116500392-0.04145480017720.2118267069220.7173689798690.080259113452-0.1763342309111.20022712641-0.08374081366321.1105580463422.432249576439.90400951136.2524378882
328.80234251871-1.85832919572-1.998158024258.05591744432-3.075969272782.570093217530.1667659458590.1680992426140.03624624149790.9185648036890.0914519807791-1.05763834942-0.1779205619420.567875579637-0.2457234793630.4294039685680.0865727955706-0.2277567776680.971379781045-0.2350003047421.0377250125818.512893452243.283454939123.7662975531
336.195275592980.210151824386-1.678444364465.47526790912-2.298107041395.074158908780.403773386454-0.3110204193420.591224378709-0.0139990631762-0.340093147629-0.416517045848-0.4732566132890.294492180727-0.06224455311640.4159842315070.032549450749-0.2102516284130.75758969564-0.06922339254580.8034470348328.3146838693547.50146000627.009896544
343.85584618491.223594531011.890745764110.9083945396790.5812288453541.810272632670.3739198477890.211904385399-1.557759841130.216275287474-0.0213856460955-0.9886319526040.7220837906240.779710484624-0.1635111100860.3899122211630.215026425395-0.09555900845771.03240975943-0.01427186297951.054815197239.2515700062332.869245290325.4371885424
355.153053799111.34587372845-0.8388299183183.00774086924-1.56520115884.25928768270.4601384598331.697304542550.530393370997-0.354472208482-0.452350712904-0.696853557129-0.1786523502570.190649974856-0.1620547402380.5118414337920.2982531305960.1174186355911.391837167090.07504797080930.863162359622-45.205030351969.987209224611.1583948468
364.06935724323-0.869397945502-1.328826643231.079131196240.6475449640681.588436731440.2995349022750.52925988222-1.022908626630.244580156728-0.163749729232-0.4151100808420.5022748104920.561550626348-0.1214227597320.5143340480540.215814311651-0.2968473433370.962779174272-0.332289492831.44179900245-46.060283806252.78257034120.4462577817
375.045810190461.242236386592.579985772212.94701702765-1.87000717227.22491465289-0.2532263910982.171031602580.225689736608-0.215916022861-0.173532755169-1.65863671290.6757037626081.009601720220.3081394781270.5606612506330.328076305119-0.009010275123681.45698062045-0.3670279854621.08547310126-39.548626176754.853738861814.0392869599
380.261560522423-0.287516649684-0.1702833142993.53349622997-0.03847540300380.1221860971570.140879268678-0.259242462295-1.135687996760.6438007928450.807977339853-1.006553897060.3372546271640.286103962585-0.6683638986760.5926270902920.114308796467-0.3509563442860.833869546953-0.2689272454722.0970512555-30.980082201156.982626105231.1478830228
396.499606926832.45449942311-2.929397358193.494577866991.552826711994.07179149164-0.1608218047840.620760059936-0.5952661263420.702517248315-0.250693753708-0.2563569928940.4105805094440.6296176678320.2995833968960.3221666503650.141769258543-0.06452029797790.8153383042560.03086394508161.24963576519-39.054125032861.528941751531.3081451796
405.267017375950.227902226812-0.3774803748560.370994292810.3800787628942.603915982460.1947308530010.5191617066830.3765744718180.08218781461490.0142011169149-0.3707576846720.1392306288150.246893872177-0.08607823462450.2970005180780.110990118831-0.218183419070.666122521321-0.05186519356631.22648215103-43.981985941765.673925622732.9876454679
415.991837247842.58295422631-1.326613951075.02682245893-0.7495181821122.49070962667-0.004550351490930.3113146226140.2880542538920.3348270562670.2696142517760.1310618380090.2518638991180.0738203171129-0.314757760240.5875412023590.0405336309909-0.458451472510.70046763672-0.0592133005061.27654222163-44.426151009566.264205114243.9164581907
426.28115110672-3.325535761320.003856959392766.267267442883.683098416526.21465238574-0.198757851611-0.0345060493448-0.6306147287771.007680648930.117867728650.1176372098450.5545390065230.1036344000290.05250736277430.5502819988620.0148022205659-0.2176850477260.521163551795-0.1500980019980.977258421125-59.531947459559.602379007540.636752623
432.26139514985-1.936478525571.11900237883.379488947990.02177340722386.308825039120.5426293067661.298100921940.6626442963230.211845916818-0.60926893486-0.338796897102-0.000830272694202-0.105410855731-0.113059767920.2791884234670.131115415726-0.00750234965020.800141616488-0.09560227403940.805867943188-51.494710848166.646120402621.9428555271
442.63952817519-0.08675148413290.5534661375036.66568589563-1.234144721412.416975937810.04072516344931.197786115141.107290012490.1825108420460.0927280495569-0.360311298618-0.379610774356-0.51454289690.1192335614130.2935421620080.077879176084-0.05309825891680.792230229079-0.003780048442121.07993053908-54.13601669473.035365288529.7990685925
452.654431245740.5247817695050.4144890605132.342685166870.08083475976472.452241129180.07982979213211.51186307659-0.8329441163050.0995410011388-0.1577358028640.2433865800730.615792561411-0.31901106984-0.1796920745740.5376078931630.164783414597-0.3947024459811.22420613756-0.5302673866621.41668705486-62.804971543249.832544903417.2305566781
462.065981511150.3159482920442.924688351464.569500486730.2307249263074.153932055830.1589923123082.61470156608-0.586577266199-0.6142076543250.256882258096-0.2822229613260.6344434717880.473607906093-0.4392172401290.8949993385550.0766278967774-0.1278295990522.44209122786-0.796989619161.26429805725-52.942084823955.11065291183.39802047606
473.399566725750.5209214773733.400463547930.1521069162480.4765035328753.410464434570.1180559836890.318912078136-0.422547908568-0.2377902362550.19964082022-0.1180094180140.608011633297-0.201182555428-0.8464095836560.610854638299-0.0227747404806-0.4877717325071.50386819434-0.77890217151.55271675302-59.927766646745.15015896968.68853929812
483.20133484314-1.58626404592-0.2992025413672.027637761570.04540088116480.03466878980470.2426951644463.04271185076-0.323433268712-2.01202741772-0.04165043197520.4356935918680.488907861279-0.92693921598-0.5311206033021.02812892813-0.0636721119142-0.2035699897232.06392072032-0.2225550904171.03656057845-74.913270494952.007856942-1.20736231237
492.423668690541.26168371081-0.2136581581221.10144433952-0.4473882528670.264529680564-0.0193821406341.154851321190.0447310234324-0.71207228282-0.1026248303970.4379203765280.416269971274-0.223679340843-0.285770164950.4227570809460.190447072915-0.6232358994891.69740814507-0.5718914351751.40124359974-73.785660500260.34824707769.65571736113
504.25833722814-4.784026148852.156096583695.48385168285-1.695304697076.160166048710.8203719039691.87033114126-0.101448051005-0.00352199780482-0.355413714607-0.499753451730.4070414797011.11074124619-0.4998172175340.6687596658320.0845034789865-0.1636765699431.25852462978-0.2427214714011.00174033287-80.108667074970.07817033517.9839341828
511.01158375957-1.19931353413-0.4295195396652.242101760860.1887803310291.463645319720.1829515523070.8283632989560.359249571289-0.2649870217230.05339402188120.00162962607461-0.173341999879-0.429434650698-0.2850280065970.4457282014430.136527867533-0.2103678095211.2930826457-0.01095997599551.02421536068-65.162648288772.703298761214.1786920291
523.32670553766-0.06142206638160.6847987918711.70960744596-1.301365187381.1184864621-0.1430400331520.4255959592230.0384094469913-0.113773143139-0.3352119217320.4229363491750.119232656886-0.249672985457-0.9183302758890.340149276960.450737742946-0.4257437695771.21616736947-0.3611866105951.05839525879-71.726205583765.31990550423.4449886307
534.07500826334-2.214249506960.4859073244013.643949085322.583092868233.375235768770.460550258562-0.666511032704-1.335936248450.389637167266-0.1590140907650.9481222696990.363952936814-0.3995258636620.4496651824830.809916010534-0.173902216951-0.2446787087110.3513227381940.1085983071870.617136515236-37.851052340252.518928584183.5955049125
540.6344922434950.03870969883910.5061158919080.04252756431210.0421274937830.4007573909510.212304605512-0.088613321378-0.849693743022-0.3921489195930.2885438562540.1870972193840.369720279573-0.0836556375370.1006183162230.9712456310910.017448713354-0.6158063305770.331092011084-0.1414294041.39134475966-29.3531778144.794207744468.7967873014
555.580689491653.206817244180.4373987355972.461308396971.137951086181.315896635480.1888871021240.451727104936-0.477355138481-0.579306931979-0.2321582327030.2749405091480.0830893927419-0.3841053553310.01919830732280.779814389379-0.0210494685271-0.4870259955180.2306131813010.03957172105070.966380474019-33.491120178958.295028673362.874687998
565.544089092462.15903945032.047202860213.489134870250.6375263979742.081000753320.4297402062240.9493691202350.113784683926-1.21999959745-0.01741227978420.676696571875-0.1516107618180.306040111491-0.402639081771.312939798650.135884933954-0.6868532051980.629408205959-0.06803212832451.24135229699-31.763665995666.955977297854.8429001163
575.20476779651-3.477193465962.379739410485.680743649520.6465740096762.66365221343-0.09757002776270.8507912212710.428957173698-0.310904582252-0.0911690137847-0.375795077725-0.1855489021330.475876278792-0.07910579664140.6854596635540.0107405464155-0.2069398660570.3747404083160.003660672246640.972429765412-15.928557258568.067092298262.2933175348
583.63410304-1.00686121474-0.05681201020490.6257521912-1.15523266284.135052578350.294178620659-0.1795706235820.0642681452846-0.0774663448426-0.4616747294620.285312088621-0.439187261611-0.1845651984980.3776828123480.734761197892-0.0172062613817-0.3782756842750.3618116858360.05215471059610.956875807786-29.681788443963.789639846574.7170125349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 186 )
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 233 )
8X-RAY DIFFRACTION8chain 'A' and (resid 234 through 250 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 13 )
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 108 )
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 154 )
12X-RAY DIFFRACTION12chain 'B' and (resid 155 through 187 )
13X-RAY DIFFRACTION13chain 'B' and (resid 188 through 213 )
14X-RAY DIFFRACTION14chain 'B' and (resid 214 through 232 )
15X-RAY DIFFRACTION15chain 'B' and (resid 233 through 250 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 31 )
17X-RAY DIFFRACTION17chain 'C' and (resid 32 through 60 )
18X-RAY DIFFRACTION18chain 'C' and (resid 61 through 95 )
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 123 )
20X-RAY DIFFRACTION20chain 'C' and (resid 124 through 154 )
21X-RAY DIFFRACTION21chain 'C' and (resid 155 through 172 )
22X-RAY DIFFRACTION22chain 'C' and (resid 173 through 213 )
23X-RAY DIFFRACTION23chain 'C' and (resid 214 through 250 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 13 )
25X-RAY DIFFRACTION25chain 'D' and (resid 14 through 74 )
26X-RAY DIFFRACTION26chain 'D' and (resid 75 through 95 )
27X-RAY DIFFRACTION27chain 'D' and (resid 96 through 108 )
28X-RAY DIFFRACTION28chain 'D' and (resid 109 through 123 )
29X-RAY DIFFRACTION29chain 'D' and (resid 124 through 135 )
30X-RAY DIFFRACTION30chain 'D' and (resid 136 through 154 )
31X-RAY DIFFRACTION31chain 'D' and (resid 155 through 172 )
32X-RAY DIFFRACTION32chain 'D' and (resid 173 through 187 )
33X-RAY DIFFRACTION33chain 'D' and (resid 188 through 232 )
34X-RAY DIFFRACTION34chain 'D' and (resid 233 through 250 )
35X-RAY DIFFRACTION35chain 'E' and (resid 2 through 31 )
36X-RAY DIFFRACTION36chain 'E' and (resid 32 through 74 )
37X-RAY DIFFRACTION37chain 'E' and (resid 75 through 95 )
38X-RAY DIFFRACTION38chain 'E' and (resid 96 through 108 )
39X-RAY DIFFRACTION39chain 'E' and (resid 109 through 123 )
40X-RAY DIFFRACTION40chain 'E' and (resid 124 through 154 )
41X-RAY DIFFRACTION41chain 'E' and (resid 155 through 172 )
42X-RAY DIFFRACTION42chain 'E' and (resid 173 through 213 )
43X-RAY DIFFRACTION43chain 'E' and (resid 214 through 233 )
44X-RAY DIFFRACTION44chain 'E' and (resid 234 through 250 )
45X-RAY DIFFRACTION45chain 'F' and (resid 2 through 62 )
46X-RAY DIFFRACTION46chain 'F' and (resid 63 through 74 )
47X-RAY DIFFRACTION47chain 'F' and (resid 75 through 95 )
48X-RAY DIFFRACTION48chain 'F' and (resid 96 through 108 )
49X-RAY DIFFRACTION49chain 'F' and (resid 109 through 154 )
50X-RAY DIFFRACTION50chain 'F' and (resid 155 through 172 )
51X-RAY DIFFRACTION51chain 'F' and (resid 173 through 232 )
52X-RAY DIFFRACTION52chain 'F' and (resid 233 through 250 )
53X-RAY DIFFRACTION53chain 'G' and (resid 2 through 31 )
54X-RAY DIFFRACTION54chain 'G' and (resid 32 through 108 )
55X-RAY DIFFRACTION55chain 'G' and (resid 109 through 154 )
56X-RAY DIFFRACTION56chain 'G' and (resid 155 through 172 )
57X-RAY DIFFRACTION57chain 'G' and (resid 173 through 213 )
58X-RAY DIFFRACTION58chain 'G' and (resid 214 through 250 )

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  • 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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