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- PDB-8u3n: Structure of P450Blt from Micromonospora sp. MW-13 -

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Basic information

Entry
Database: PDB / ID: 8u3n
TitleStructure of P450Blt from Micromonospora sp. MW-13
ComponentsCytochrome P450-SU1
KeywordsOXIDOREDUCTASE / biarylitide / crosslink
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
beta-D-glucopyranose / PROTOPORPHYRIN IX CONTAINING FE / : / THIOCYANATE ION / Cytochrome P450-SU1
Similarity search - Component
Biological speciesMicromonospora sp. MW-13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHansen, M.H. / Cryle, M.J. / Zhao, Y.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190101272 Australia
Australian Research Council (ARC)DP210101752 Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Structural Insights into a Side Chain Cross-Linking Biarylitide P450 from RiPP Biosynthesis
Authors: Hansen, M.H. / Keto, A. / Treisman, M. / Sasi, V.M. / Coe, L. / Zhao, Y. / Padva, L. / Hess, C. / Leichthammer, V. / Machell, D.L. / Schittenhelm, R.B. / Jackson, C.J. / Tailhades, J. / ...Authors: Hansen, M.H. / Keto, A. / Treisman, M. / Sasi, V.M. / Coe, L. / Zhao, Y. / Padva, L. / Hess, C. / Leichthammer, V. / Machell, D.L. / Schittenhelm, R.B. / Jackson, C.J. / Tailhades, J. / Crusemann, M. / De Voss, J.J. / Krenske, E.H. / Cryle, M.J.
History
DepositionSep 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450-SU1
B: Cytochrome P450-SU1
C: Cytochrome P450-SU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,44914
Polymers135,8263
Non-polymers2,62311
Water6,287349
1
A: Cytochrome P450-SU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1114
Polymers45,2751
Non-polymers8363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450-SU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2276
Polymers45,2751
Non-polymers9525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450-SU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1114
Polymers45,2751
Non-polymers8363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.078, 95.748, 105.217
Angle α, β, γ (deg.)90.000, 92.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 32 or resid 34...
d_2ens_1(chain "B" and (resid 14 through 32 or resid 34...
d_3ens_1(chain "C" and (resid 14 through 32 or resid 34...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TYRTYRLEULEUAA14 - 3235 - 53
d_12GLUGLUARGARGAA34 - 9555 - 116
d_13LEULEUGLYGLYAA97 - 127118 - 148
d_14PROPROGLNGLNAA129 - 163150 - 184
d_15SERSERVALVALAA165 - 169186 - 190
d_16SERSERALAALAAA171 - 215192 - 236
d_17HISHISASPASPAA254 - 267275 - 288
d_18ALAALAVALVALAA269 - 294290 - 315
d_19GLNGLNGLYGLYAA297 - 338318 - 359
d_110GLYGLYLEULEUAA340 - 366361 - 387
d_111LEULEUARGARGAA368 - 393389 - 414
d_112HEMHEMHEMHEMAD401
d_21TYRTYRLEULEUBB14 - 3235 - 53
d_22GLUGLUARGARGBB34 - 9555 - 116
d_23LEULEUGLYGLYBB97 - 127118 - 148
d_24PROPROGLNGLNBB129 - 163150 - 184
d_25SERSERVALVALBB165 - 169186 - 190
d_26SERSERALAALABB171 - 215192 - 236
d_27HISHISASPASPBB254 - 267275 - 288
d_28ALAALAVALVALBB269 - 294290 - 315
d_29GLNGLNGLYGLYBB297 - 338318 - 359
d_210GLYGLYLEULEUBB340 - 366361 - 387
d_211LEULEUARGARGBB368 - 393389 - 414
d_212HEMHEMHEMHEMBG401
d_31TYRTYRLEULEUCC14 - 3235 - 53
d_32GLUGLUARGARGCC34 - 9555 - 116
d_33LEULEUGLYGLYCC97 - 127118 - 148
d_34PROPROGLNGLNCC129 - 163150 - 184
d_35SERSERVALVALCC165 - 169186 - 190
d_36SERSERALAALACC171 - 215192 - 236
d_37HISHISASPASPCC254 - 267275 - 288
d_38ALAALAGLYGLYCC269 - 338290 - 359
d_39GLYGLYLEULEUCC340 - 366361 - 387
d_310LEULEUARGARGCC368 - 393389 - 414
d_311HEMHEMHEMHEMCL401

NCS oper:
IDCodeMatrixVector
1given(0.524318461955, -0.839114474557, 0.144834557483), (-0.84533132249, -0.533394938752, -0.0300798026922), (0.102494417749, -0.106661792136, -0.9889985624)-50.0648474065, -85.2518398806, -70.3345993397
2given(-0.449860496459, -0.893085315345, -0.00491459465848), (0.890676703228, -0.449038659313, 0.0711287056625), (-0.0657308455232, 0.0276206798737, 0.997455038581)-94.4647065985, -11.1408267315, 34.8106838165

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Cytochrome P450-SU1


Mass: 45275.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. MW-13 (bacteria) / Gene: C5N14_21030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2YLT4
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 357 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris pH 7, 22% PEG3350, 0.05 KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.15→47.87 Å / Num. obs: 65730 / % possible obs: 99.64 % / Redundancy: 2 % / Biso Wilson estimate: 34.21 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.0615 / Net I/σ(I): 5.63
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.3549 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 6446 / CC1/2: 0.662 / CC star: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.87 Å / SU ML: 0.2832 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 1994 3.03 %
Rwork0.1938 63709 -
obs0.1951 65703 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.38 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8645 0 174 349 9168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929081
X-RAY DIFFRACTIONf_angle_d1.083812436
X-RAY DIFFRACTIONf_chiral_restr0.07011393
X-RAY DIFFRACTIONf_plane_restr0.0111651
X-RAY DIFFRACTIONf_dihedral_angle_d13.21373311
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.731876982792
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.640198996749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.3141250.27594013X-RAY DIFFRACTION88.02
2.2-2.260.30351410.25744600X-RAY DIFFRACTION99.96
2.26-2.320.27631470.25024531X-RAY DIFFRACTION99.94
2.32-2.40.28831420.24224566X-RAY DIFFRACTION100
2.4-2.490.2911420.24034579X-RAY DIFFRACTION100
2.49-2.580.28781520.22614595X-RAY DIFFRACTION100
2.58-2.70.27381330.21454575X-RAY DIFFRACTION100
2.7-2.840.28591550.21754576X-RAY DIFFRACTION100
2.84-3.020.24361360.21924581X-RAY DIFFRACTION100
3.02-3.260.23651430.20784583X-RAY DIFFRACTION99.94
3.26-3.580.24881420.18424606X-RAY DIFFRACTION99.77
3.58-4.10.19191480.16254589X-RAY DIFFRACTION99.89
4.1-5.170.18041430.14924627X-RAY DIFFRACTION99.9
5.17-47.870.21661450.17184688X-RAY DIFFRACTION99.88
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)
13.32004304877-0.788911188257-2.724323622138.58980287832-0.4766319321222.85625545554-0.0819380026112-0.3806860132920.245119116040.9979684287740.302166477556-0.0512513251870.04490049725620.957913011865-0.1174410597720.352466651372-0.0176642723626-0.05857784769680.505973376354-0.09198179805530.249008836108-11.6320300026-17.7017849717-19.83747152
24.62641396815-5.56537279007-5.916459105117.660896093055.700931706019.633246135450.7611949066640.2304278414640.0473061943585-0.1502789509790.424319057217-0.9701551446440.03109172253742.68558549789-0.9916109827660.4994486306340.12812875369-0.0967378243520.979186496546-0.1553855414820.402487894067-7.85683051603-22.5501748075-28.0030828489
33.380549698361.50934820235-0.9716440896682.319842747051.035450608865.74477054290.458834011296-0.275314479018-0.03669532953310.668828712142-0.0396131275827-0.2987999334960.6920207193681.51618650818-0.4526337635370.482350178640.222069948896-0.09741931239720.787790285151-0.19805551850.440772749178-9.39214630896-32.1866786494-24.5719737154
45.04565149269-0.120271839747-0.479701064062.90342493246-0.6148033286160.210873299146-0.0102966347994-0.452532191769-0.3417633203990.0978132925020.222161083620.2464341077411.033371518180.538511269142-0.1202015216670.8702394357640.170939183341-0.1430471386180.3525802468940.001692709183790.359508418178-26.5889162244-41.6704848102-22.0142924031
58.87396317118-5.42058461214-1.1860009353.67199234526-0.3585710501273.470775468970.630291500983-0.336292308395-1.148500830431.44203177173-0.9927985151120.223322906380.9520727786710.4619595166380.4676995970610.745978939041-0.0482700898177-0.1688637151750.3420455661890.0613326553930.553835932904-36.9524250537-40.7114353121-27.6752244953
62.663490317921.06256468241.540722361159.534721993230.5388999220623.78679916194-0.0634311222425-0.1174856376980.228622078720.226782704292-0.2200045174660.736465864114-0.0152833438307-0.2168967238120.2752397431230.218251482401-0.006776223795640.01324122603150.270022447386-0.05841852747990.416844803356-43.7476334278-17.5801005442-31.0168428782
79.15127805968-4.389413778852.013950485127.24027125098-3.399761852442.84037323379-0.350739347468-0.2287800362930.6387526090260.3829632954850.2603044233491.12967221702-1.29909878677-0.06380471970.0705887231570.528766690993-0.00233994959493-0.04035101010730.377813887594-0.1118638019480.518067433255-32.1019322810.572572818181-20.823554588
85.980093755871.91236041906-0.02793218867853.87824383606-2.244690322845.99843950944-0.0129472618454-0.4675516507480.649791319510.47070551511-0.1780945644150.629685641234-0.449662824734-0.1143763995810.1591143323860.2953018516640.04247301363810.02374176799480.242451332547-0.1198667658550.381288061009-40.6819948237-15.3083177276-22.512768461
96.1587515762-3.095092240824.175824291426.82236202633-2.694880814998.33161390318-0.380537840924-1.034261310750.379664669171.433525273050.2387390341790.444862506703-0.388071768774-0.5573549216290.1580219859370.4765948564130.01057421569140.09402681808270.426264841894-0.05936755901670.295662899872-35.3768415252-18.1400214784-12.3141005318
108.51860290091-4.794753086432.89730633314.240720196830.3138396550693.40788161647-0.429525993965-1.108667837840.230258948596-0.3713006396470.610879088825-0.1647928051890.309415861363-0.705664850829-0.2152814175860.5463662094650.0222085399475-0.0446750299520.489160314066-0.02204057259320.373408930692-22.1142826604-25.2149136975-9.4285007109
114.02592335737-0.5343272231736.085576373849.64244730948-3.259805925369.84887050580.123770590452-1.14787072980.4990897723370.8607903687290.200843882783-0.304612553385-1.09401599994-1.08557690546-0.285791999520.650473919840.004375401361260.0564113914610.585488937493-0.06322392839410.338052317355-35.338934918-27.3531347877-8.54776861489
126.206018846411.40168727815-2.624182390894.055521509080.8861546628581.693276942190.272317792641-0.4851634631910.537782244470.0601060626420.01785570954630.612166024568-0.0922634372898-1.3323188092-0.2125328093360.423900042626-0.07039503966930.3006656020110.8140829370490.0975259803950.671643750584-49.5711985403-27.0536204506-16.6980819629
134.109378938812.65078682694-0.4328565365636.47279239421-1.724002009244.27617254648-0.065209876392-0.191215311473-0.2641053449560.258656356152-0.0912902520669-0.01742222488410.17113226828-0.4260550967580.1847683313370.2357771159770.004245519420780.0637749611110.249050576561-0.04419217643340.252315456936-37.4131116003-25.2676966298-22.9698577241
142.858166395540.7106552804773.23177209122.958957055953.715902122526.93531421909-0.107700436794-0.0425773810983-0.386692121101-0.123474177859-0.00984550528868-0.185608392736-0.490290442747-0.3240267652910.1497070078950.649173290047-0.1642252912190.07518647046410.4225861637750.03054725623920.515228466569-26.9259040514-6.1628169592-39.3262016172
152.18389359713-0.7577287597630.6189911380543.82379109701-0.5609439052922.591956415560.1640422365660.190549656964-0.1835186374480.1800918800860.139166496889-0.2374890242160.4106576728330.932640280364-0.203301520580.3381549387530.0828400477076-0.08360358781090.46523512745-0.07099018163140.244271247097-17.720115927-27.5237320091-31.8837971305
164.21297438564.59605067098-5.514618355165.27940641938-6.586485587558.396522049440.1056450715730.1691503233120.738517089168-0.7533687372710.3192032971240.2346133712490.5472031747890.129729947469-0.4664454966960.423783876115-0.01785681969540.02888548606490.318108466483-0.01140631665290.409470050233-22.1807973265-23.7293840763-41.4757545954
174.89126256553-4.12165567791.841761899119.17333208763-1.058020888494.460372621420.04020643561270.279936310547-0.0739204447-0.675791030025-0.1581511299470.290085107450.06752404367150.4186567200630.1265139073060.21753491808-0.0214488444664-0.009396668914160.249807301192-0.02925969376370.197887132722-33.0378994008-20.1285394452-33.8921608853
186.687937354446.503554567232.809879765988.23396626612.151711379132.254866726550.1066973499320.7639803541191.53131069194-0.752711195206-0.9264526674731.33713733545-0.4684682123921.000195945280.6954601985580.809736565206-0.0429764747852-0.3382426505060.425052565160.03460267885780.746736227158-33.72174068812.91877797892-33.446243122
191.19329670619-1.15173246329-0.1062023524312.45406483377-1.575313246282.128839433220.0439511379569-0.1180093196930.1712364065690.1459896164330.1054584442830.210500306025-0.1034791091270.305247844366-0.1073769103790.277496224933-0.00972686320738-0.04764094136980.343797808909-0.07339906221510.35776525943-21.9473877206-11.0173026181-20.3087407965
204.78102247277-4.002982563274.277324457053.33936605557-3.569445764673.8338346-0.8135993917770.007124106415261.336004240031.11429840479-0.492017689038-0.113778567257-1.918391546770.1815440362971.041455100120.78220922499-0.0675633532869-0.1443199061170.317022506852-0.1084172178660.570241301215-27.0474273830.877000935907-23.2565856725
211.264962089472.444797857420.6465318340445.35867281184-0.5193654330375.452278146110.1629668813020.0160703279494-0.230440299280.0219280990651-0.209513165844-0.3843125000410.8858678120250.2748847101080.1163372111160.4734655757340.07322349190470.0951548851780.204267705271-0.004346980283860.40682539448-43.3469060056-65.0704737187-49.3331283578
224.65127562355-0.813418414872-3.32462790813.2378037846-1.197557869596.86685624158-0.287630543168-0.223669505544-0.679188889880.16448306337-0.00181902100602-0.2028646263010.9465647845490.7643121712840.2378317788930.4223502579670.0908460748349-0.07931707921240.304699369290.007031926668460.416907680202-33.2864935762-60.5062771365-42.2565579635
235.12726946168-2.332871280942.623193283985.93626325943-2.707251582754.871345938410.2952504259310.4622122161670.384547920459-0.230532640017-0.239495838608-0.5165837770.07947025525370.7441983986090.0266316282780.3351795473030.004959418085090.06900289221160.317727172394-0.05015817655940.389596547682-31.7151864847-39.8356942625-47.6814990842
242.70525539-4.62007737323-0.7301494309958.297290421332.378926565513.84577054782-0.0405092927852-0.02388028559180.995234680148-0.2407650772760.123302928414-0.426452660552-0.166764186720.257088139775-0.09282542923810.283922501869-0.0320996157505-0.08063745571520.189547219194-0.006222764455340.509272811455-41.6324620213-31.8163121254-41.8072803603
259.724978272926.462274115131.182791175984.523786555090.4303615781230.715783589989-0.407487439708-0.546818190330.0382720893287-0.774507912245-0.367930009392-0.404148938115-0.773117145094-0.2340102231170.4728580689980.5688866299330.118906963882-0.02332298216690.568042266718-0.3404661865020.983440923994-59.8739317495-31.8136881794-38.1094971296
262.9922600764.196565254231.28441109395.972991661421.342561617844.61512321488-0.0028924073276-0.4517390372930.870832303761-0.2631247877860.2700308417940.271199251863-0.62750800450.0959747635266-0.1981119087650.301163699040.01217158440880.03281671913540.462408429829-0.178584369690.487117125431-69.1987373531-43.5284731669-44.9565685784
273.821074709350.482339649565-0.4830815185545.68768116459-0.1395271826533.72645580070.0551321051640.370739253172-0.0924436902257-0.534246066331-0.0278305367840.3526219971570.305893391361-0.48084874014-0.001937544771290.2342576415340.0212723759317-0.06949534693950.261353844597-0.06123234145390.261782862828-64.1435265728-46.8373942097-53.0920259808
283.51249174112-5.62835252262-0.9999275769319.222451480972.49381370615.285030696220.5110596143280.9075468961350.251246710173-0.199243643347-0.377716034829-0.3181826093740.09070994067080.384065262519-0.1130500981040.3989694437090.05424723034910.0145239301960.3518131944720.007461773658470.256699576521-45.4850379423-50.930663782-60.3264233539
297.98079225175-5.30878103501-2.37780474264.137609780792.957062489594.296875522050.4759524342130.6804581039110.7002212367-1.0672017562-0.409452254107-0.438940627303-0.59191248339-0.289195618692-0.09258828140330.4928807613370.03970638521230.01075430421730.3076386162210.1593371135670.434288961771-51.1151645712-34.3133034988-60.0119081296
302.1439253609-1.81299124867-3.001804364514.23086793893-1.040202890678.957182141770.4020522761870.2327209238691.075959472330.267163829334-0.1189835753441.52945036916-1.02501878198-0.919872867793-0.2138393688140.5639703145270.110952313113-0.1722537588630.222057494731-0.1189353322580.851828247701-54.9418363851-25.4483756983-47.005145596
311.871989536270.1688447581920.05692932180573.68880840321-1.276111556832.613781506480.0280127894051-0.2381317739580.347975674868-0.168735017045-0.33159240141-0.0123598174369-0.1831641635540.0277457234050.2827092823170.279144246446-0.01736939500720.01570571083720.169976876207-0.02530715943530.30899371624-50.6362227483-40.6064838992-48.6285436901
323.597515484721.652731691111.686329227856.097807242765.479557155725.58758217010.511755128034-0.2131179660640.2024810217350.14687725845-0.685075587186-0.344504021519-0.0120138271548-1.407983754770.1237681355220.655659280694-0.0721404701045-0.03466999036280.6962948924840.2077850599970.381000684772-64.4331629393-57.6162822107-32.9713015228
335.086119834792.56956708648-5.305888285413.32677765209-2.949825297117.80763612114-0.15442970006-0.2255425569070.1271081569110.1068042119960.2347339829530.0965982667250.284351208569-0.273807304652-0.09210837838840.316958384116-0.0135886940651-0.04178476290320.3071111900510.01966621318540.24480893079-52.24299156-53.1135127642-36.7500753812
343.63817611196-5.22325412023.172260749817.6240200659-4.080605416566.5321277645-0.00542566010151-0.75632409962-0.02415271783260.1346557662850.357802019254-0.6793606587350.4596163447550.898901582666-0.3135064622330.3152753839480.0606943932141-0.004003394222450.518490825779-0.04929771369180.414922790044-25.0551552695-50.263439802-40.5175170014
358.94497485583.34350114271-5.445187814283.29436817105-2.932150199096.55959659327-0.0066557456054-0.446906932078-0.3964841634790.184220506229-0.0981258435952-0.2563266950180.4555971881210.1508981082280.03319188701710.371216389791-0.0112573787003-0.04722039445550.16980567141-0.006344747332670.234775376597-42.5285698244-56.2223543592-35.2033368735
366.419349484073.10164093362-0.01708872772952.960561630640.05056765614042.978118011810.318803476846-0.2060627662130.0748049350510.36762732118-0.23594533297-0.164810781843-0.0808125038275-0.178956446123-0.07093506875520.350520271125-0.0562380199114-0.01799191255750.200556525683-0.07789551936230.330286938486-50.2151260662-43.2767591186-38.6900143493
379.401052750140.973067667406-5.135895034155.62513699379-2.608096901227.353288291940.258827176261-1.510900741060.2569226640030.734497664662-0.444840863053-0.06103421433180.006791651740.1489937922670.09797225328350.249970945848-0.07977258405240.1321846472040.608121878416-0.1218869596060.256111132119-67.7376515304-50.1099674553-37.4801560334
385.4053102216-4.63618265563-4.856034441614.38007712644.095772056145.90151800362-0.396454936837-0.532412815087-1.542501681860.3133230390860.3912241506311.776788348151.48569544924-0.7027597457930.1174283190940.717102530079-0.1974358312440.1888040971720.607041449231-0.06477915259451.1397453469-72.5861999862-60.084606396-42.9527808446
397.457664967960.2413718612491.038852160863.169288736332.152738336174.135373111040.3623461114010.244828951627-0.785466440169-0.681188603063-0.1840383107670.6082542100330.617490516704-0.385759998664-0.156005327240.5505083388160.000961019514522-0.122298234430.221181909090.046435311120.424711791723-54.2399750012-60.217103259-51.5582920079
405.430034075341.681034706716.487515293815.614476663370.5543834146938.16338071061-0.485130283207-0.0354539898854-1.249870935370.07714912628590.7476700428411.249381742980.952589624011-0.570729801893-0.2768181018550.539439834392-0.12127934720.02767220476420.2826443018050.08575834897020.720990454303-68.2012130013-62.3187053018-50.0233667157
414.444448225985.75433135648-3.319852411367.71812259342-2.870251471239.91247940473-0.0049711991178-0.998802787991.37912030004-0.271880332801-0.4384902142780.892221466385-1.002951175120.1282181205250.5198588641070.6762808984750.178089322405-0.1138420420810.532552077463-0.1198587879120.477685807035-72.7077824723-14.024122901318.7404891457
423.700059607293.54890830093-1.482951147514.70708625464-2.132506956821.22110503034-0.7413495825-0.3638918168120.522132931039-0.4387325216810.6376614761850.345374454778-0.199298001347-0.3456329265940.1806087331510.9761071520120.19439201984-0.2518186971750.391109991416-0.1445735708550.482508605659-72.9704466977-13.99898578699.7729773553
431.20217213959-1.204016412370.7606058376321.87544604011-0.4340237580720.875789882837-0.593580759240.328777092661.051116969880.5750039784760.0047020976977-0.655371343302-0.9126559472920.4797088163220.2520608977661.01930938309-0.107989953135-0.4105444787310.3492955870520.07286881074580.913398625237-52.8823493008-12.512206351311.6962014503
448.27725727948-2.01228359137-2.778347069482.304898204454.192325588457.89578208705-0.05685248369730.4769051413050.604321448352-0.09241369138850.282062348984-1.09002018726-0.5691804357260.970231847638-0.2026081570190.499953903685-0.0192808762089-0.03464303070330.6484990355350.2197097123030.558044704635-41.7725259245-26.60361637829.2087591476
459.554309698035.99195158467-1.186849074774.67880335553-1.11089308654.08466235669-0.4663309562570.756954575222-1.62444745829-1.339516027410.271656254991-0.01886098158170.7894038206650.2622790974380.1552233923380.8465447547770.0904252024789-0.1361111960380.384641258108-0.1291028262640.717181914116-55.3999405296-43.86133569534.48697891829
465.770793503512.05825191178-3.953510370062.67152659595-1.430379245752.95750836077-0.50272477961-0.03198559369290.1642937837262.171489904690.989996307327-0.135395169518-0.708712262475-0.666562492397-0.4964010025641.08253451363-0.0907391344671-0.264214985730.6516027929020.3417772949041.08184418101-76.1141155001-47.744106560412.8375218322
478.69182228031-1.29190670675-1.554242847660.5398471402340.07784412364083.99545163123-0.234213443056-0.806900424004-1.227125238060.05585342747790.4064194698280.4409708825280.575422519182-0.208646422018-0.1672909296810.518929738912-0.0216175302979-0.09922674460930.3273964825680.1642480683140.574749382339-66.3548114416-41.039786230817.1433043724
486.0337209386-1.58580603752-1.643272574475.401181514654.796944790414.35573883283-0.125581782951-0.4088771309850.2215843914570.3658397008910.0136149521812-0.1812891797870.525826982105-0.260350794449-0.01427709041920.5401411011180.118345573649-0.03634704818260.4806231263260.005377517830530.278096966518-62.0419544691-23.884748266725.9988449063
494.84571337626-5.29603196237-5.189493597845.86442547675.712067917855.59413800461-0.264866165134-2.31403116754-0.2029965921351.322419826190.788637326511-0.8676750677560.3485847633970.507907215617-0.4577718982530.6641455580010.0497046977406-0.1598139678180.6523514116260.02745859606150.530930506589-53.5361679976-31.742136104128.0882859377
509.18755997823-1.11760980186-0.7734347364034.61654716378-5.010319322066.59331997205-0.2914806788410.3119471212-1.151105297080.6343531078370.6029444737290.05212902616751.45260878698-0.17301075331-0.3196077720560.6352666775020.0552078434319-0.07446391057560.2686687920770.0003589414050020.601396589501-47.7583174904-45.470259114419.5557091758
512.357494887462.17817254935-1.698022218562.81607549196-3.512825850525.88880181410.5594448072370.458187363675-1.32788140923-0.263160716387-0.397296467857-0.7355091856570.2001663644180.182242540817-0.1045212792560.4812023344890.0482825831013-0.08103997400320.376612075655-0.05042991495890.460599966065-41.4403412804-41.927217217612.1232202053
527.04309337354-1.708885539414.318567958332.31846284488-1.43395917284.17271315597-0.158727250581-0.3017008445790.002363247171890.2124023139260.00269855673286-0.239039790979-0.03197958150750.01859308371830.1552151038140.4737000150280.0462274039922-0.1139132078970.236288145034-0.01229479785220.318567734124-55.9372675827-32.606897070814.9163244687
538.395058701192.128266159242.340565564975.03186125242-0.5244947694272.956907357760.07288615177550.323552926622-0.437599016983-0.3819458683770.055377220172-0.1434293303170.241984105872-0.162534110306-0.1017515858920.5864390010450.0494189290827-0.1028013468880.298190057807-0.02458091658480.300766126937-68.5634569074-28.24128424851.44324825259
540.5505407722990.833360466067-0.5635308424541.24594923233-0.8578316066690.5738006658440.1049252285660.1550744147060.762206843045-0.1804447483550.209158448029-0.377421936438-0.2990841056990.2034094144760.462054455151.30599372528-0.162418795786-0.843947527947-0.3393201201610.3186897359411.74718529949-49.3932510736-4.710311090338.98936926619
554.97583258814-1.086043917751.216326675923.74266906853-1.007405666881.509173309-0.08972089301360.4068034682460.453405171661-0.103971935047-0.1222792752730.204501576533-0.4716425922430.04514754037060.2207226389390.653801180320.0440839997527-0.1717844942660.3372698065020.04307950873420.366539551382-68.4156071025-17.9472312562-0.65716487191
568.27042510961-3.5894477054.402018759722.70635344978-1.282457967545.77433103694-0.3650701607351.569784407420.0950794855858-0.83833344695-0.4799112816050.000283509899815-0.341899308142-0.05393529279640.6944883781230.618895045171-0.0993992759383-0.1137452764820.5692400247690.01245385043920.354130196394-62.2423998245-23.6945341269-3.7267294988
577.346672872276.265104242520.6528900356436.56322350109-0.6594487103383.986449907510.14488037110.789811700134-0.756895532989-0.5013465939850.1380548958440.02957306417930.11037269288-0.187834582615-0.3811572829640.5993621489760.0998685322027-0.182032353460.355722745018-0.06052818945240.481424609636-64.8856842465-36.01986185432.84281876409
583.62191449557-1.710543949925.244435499642.17657421275-2.607138463747.59700880545-0.935509684511-0.8156940530480.546631252534-0.1769613512870.4490877273490.6714841189890.239194740671-1.078200322620.5111851069580.528313413517-0.0601182378159-0.03287144363620.7324469411450.2121676865040.932736519773-83.4904844063-32.389440437313.3712468443
595.738709566454.677311487552.573203912433.842764835382.130044252211.17446140302-0.567275453052-0.840412852519-0.0644800883361-0.6478179808050.1779582001420.369289865365-0.0305880954857-0.6287664687330.3820676538180.623551635560.0696712238294-0.1561856663280.4490621582720.07246366964930.517705745793-72.1678964546-26.234405810317.2787122129
601.158809919330.711102508520.2296434645835.869034531694.991680612196.314437173950.6971113053540.131788798843-0.620975649819-1.24293645707-0.01188840273771.794205085440.767662236047-0.686242039387-0.6806970211450.7611245921830.0916996653369-0.2201744965771.026005951610.5312373190531.32825083493-85.6530845652-40.755299887810.8597952842
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 14:28)AA14 - 281 - 15
22(chain A and resid 29:33)AA29 - 3316 - 20
33(chain A and resid 34:55)AA34 - 5521 - 42
44(chain A and resid 56:88)AA56 - 8843 - 75
55(chain A and resid 89:96)AA89 - 9676 - 83
66(chain A and resid 97:125)AA97 - 12584 - 112
77(chain A and resid 126:136)AA126 - 136113 - 123
88(chain A and resid 137:154)AA137 - 154124 - 141
99(chain A and resid 155:169)AA155 - 169142 - 156
1010(chain A and resid 170:183)AA170 - 183157 - 170
1111(chain A and resid 184:192)AA184 - 192171 - 179
1212(chain A and resid 193:205)AA193 - 205180 - 192
1313(chain A and resid 206:251)AA206 - 251193 - 234
1414(chain A and resid 252:265)AA252 - 265235 - 248
1515(chain A and resid 266:328)AA266 - 328249 - 311
1616(chain A and resid 329:335)AA329 - 335312 - 318
1717(chain A and resid 336:362)AA336 - 362319 - 345
1818(chain A and resid 363:367)AA363 - 367346 - 350
1919(chain A and resid 368:386)AA368 - 386351 - 369
2020(chain A and resid 387:393)AA387 - 393370 - 376
2121(chain B and resid 13:29)BD13 - 292 - 18
2222(chain B and resid 30:56)BD30 - 5619 - 45
2323(chain B and resid 57:85)BD57 - 8546 - 74
2424(chain B and resid 86:102)BD86 - 10275 - 91
2525(chain B and resid 103:110)BD103 - 11092 - 99
2626(chain B and resid 111:124)BD111 - 124100 - 113
2727(chain B and resid 125:161)BD125 - 161114 - 150
2828(chain B and resid 162:182)BD162 - 182151 - 171
2929(chain B and resid 183:203)BD183 - 203172 - 192
3030(chain B and resid 204:215)BD204 - 215193 - 204
3131(chain B and resid 216:251)BD216 - 251205 - 240
3232(chain B and resid 252:265)BD252 - 265241 - 254
3333(chain B and resid 266:285)BD266 - 285255 - 274
3434(chain B and resid 286:299)BD286 - 299275 - 288
3535(chain B and resid 300:336)BD300 - 336289 - 325
3636(chain B and resid 337:354)BD337 - 354326 - 343
3737(chain B and resid 355:364)BD355 - 364344 - 353
3838(chain B and resid 365:368)BD365 - 368354 - 357
3939(chain B and resid 369:386)BD369 - 386358 - 375
4040(chain B and resid 387:393)BD387 - 393376 - 382
4141(chain C and resid 14:21)CI14 - 211 - 8
4242(chain C and resid 22:32)CI22 - 329 - 19
4343(chain C and resid 33:84)CI33 - 8420 - 71
4444(chain C and resid 85:97)CI85 - 9772 - 84
4545(chain C and resid 98:119)CI98 - 11985 - 106
4646(chain C and resid 120:128)CI120 - 128107 - 115
4747(chain C and resid 129:162)CI129 - 162116 - 149
4848(chain C and resid 163:183)CI163 - 183150 - 170
4949(chain C and resid 184:193)CI184 - 193171 - 180
5050(chain C and resid 194:205)CI194 - 205181 - 192
5151(chain C and resid 206:218)CI206 - 218193 - 205
5252(chain C and resid 219:249)CI219 - 249206 - 236
5353(chain C and resid 250:289)CI250 - 289237 - 276
5454(chain C and resid 290:305)CI290 - 305277 - 290
5555(chain C and resid 306:328)CI306 - 328291 - 313
5656(chain C and resid 329:337)CI329 - 337314 - 322
5757(chain C and resid 338:367)CI338 - 367323 - 352
5858(chain C and resid 368:375)CI368 - 375353 - 360
5959(chain C and resid 376:389)CI376 - 389361 - 374
6060(chain C and resid 390:393)CI390 - 393375 - 378

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About Yorodumi

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News

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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

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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

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