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- PDB-7jv3: Crystal structure of alkanesulfonate monooxygenase MsuD from Pseu... -

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Basic information

Entry
Database: PDB / ID: 7jv3
TitleCrystal structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens
ComponentsAlkanesulfonate monooxygenase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / TIM barrel
Function / homologyalkanesulfonate monooxygenase / Alkanesulphonate monooxygenase, FMN-dependent / alkanesulfonate monooxygenase activity / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / Alkanesulfonate monooxygenase
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiew, J.J.M. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1807480 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer.
Authors: Liew, J.J.M. / El Saudi, I.M. / Nguyen, S.V. / Wicht, D.K. / Dowling, D.P.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 7, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)354,2318
Polymers354,2318
Non-polymers00
Water0
1
A: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)177,1164
Polymers177,1164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)177,1164
Polymers177,1164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.650, 210.050, 94.760
Angle α, β, γ (deg.)90.000, 119.569, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 19 or (resid 20...
d_2ens_1(chain "B" and (resid 1 through 68 or (resid 69...
d_3ens_1(chain "C" and (resid 1 through 67 or (resid 68...
d_4ens_1(chain "D" and (resid 1 through 19 or (resid 20...
d_5ens_1(chain "E" and (resid 1 through 67 or (resid 68...
d_6ens_1(chain "F" and (resid 1 through 67 or (resid 68...
d_7ens_1(chain "G" and (resid 1 through 19 or (resid 20...
d_8ens_1(chain "H" and (resid 1 through 67 or (resid 68...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METHISA2 - 248
d_12ens_1GLULYSA250 - 277
d_13ens_1TYRLEUA279 - 316
d_21ens_1METHISB2 - 248
d_22ens_1GLULEUB250 - 261
d_23ens_1GLYLYSB263 - 278
d_24ens_1TYRLEUB280 - 317
d_31ens_1METHISC2 - 248
d_32ens_1GLULEUC253 - 264
d_33ens_1GLYLYSC267 - 282
d_34ens_1TYRLEUC284 - 321
d_41ens_1METHISD2 - 248
d_42ens_1GLULEUD256 - 267
d_43ens_1GLYLYSD270 - 285
d_44ens_1TYRLEUD287 - 324
d_51ens_1METHISE1 - 247
d_52ens_1GLULYSE249 - 276
d_53ens_1TYRLEUE278 - 315
d_61ens_1METHISF2 - 248
d_62ens_1GLULEUF253 - 264
d_63ens_1GLYLYSF267 - 282
d_64ens_1TYRLEUF284 - 321
d_71ens_1METHISG2 - 248
d_72ens_1GLULEUG256 - 267
d_73ens_1GLYLYSG270 - 285
d_74ens_1TYRLEUG289 - 326
d_81ens_1METHISH2 - 248
d_82ens_1GLULEUH253 - 264
d_83ens_1GLYLYSH266 - 281
d_84ens_1TYRLEUH283 - 320

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Components

#1: Protein
Alkanesulfonate monooxygenase / / FMNH2-dependent aliphatic sulfonate monooxygenase / flavin-dependent methanesulfonate monooxygenase


Mass: 44278.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: msuD, ssuD, Pfl01_3916 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A1, alkanesulfonate monooxygenase

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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: 2.3 Å3/Da / Density % sol: 46.45 % / Description: Monoclinic
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→64.79 Å / Num. obs: 75178 / % possible obs: 94.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 89.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.095 / Χ2: 1.109 / Net I/σ(I): 12.33 / Num. measured all: 353339 / Scaling rejects: 485
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.873.0110.8651.616972585756360.6061.00896.2
2.87-2.954.8180.9952.1426291566154570.6071.11696.4
2.95-3.044.6660.7592.6624599552352720.7080.85595.5
3.04-3.134.4930.573.5222692534150510.7850.64694.6
3.13-3.235.0190.4654.6125427521750660.8730.51997.1
3.23-3.355.0360.3835.624561505048770.9070.42896.6
3.35-3.474.970.2787.6623360486347000.9510.31296.6
3.47-3.614.90.19810.1122146468645200.9710.22396.5
3.61-3.784.8250.15412.520954451943430.980.17496.1
3.78-3.964.8210.1215.2219847431141170.9860.13695.5
3.96-4.174.7420.09617.2218282406438550.9910.10894.9
4.17-4.434.5480.07820.1316486390136250.990.0992.9
4.43-4.734.4860.06922.1515262365434020.9940.07893.1
4.73-5.115.0370.06723.8516001336631770.9940.07594.4
5.11-5.65.0430.06624.1214903315029550.9940.07493.8
5.6-6.265.0030.06523.9513093281126170.9950.07393.1
6.26-7.235.0380.05926.2711682251923190.9950.06692.1
7.23-8.854.6960.04630.578862211518870.9970.05289.2
8.85-12.525.1860.03635.787738164014920.9990.0491
12.52-64.795.1620.03735.7641819298100.9990.04187.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NQK
Resolution: 2.8→64.79 Å / SU ML: 0.4395 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.1704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 3756 5 %
Rwork0.1803 71397 -
obs0.1824 75153 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→64.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19789 0 0 0 19789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003220299
X-RAY DIFFRACTIONf_angle_d0.606827676
X-RAY DIFFRACTIONf_chiral_restr0.06233070
X-RAY DIFFRACTIONf_plane_restr0.00453603
X-RAY DIFFRACTIONf_dihedral_angle_d21.08257258
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.420930397925
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.445642817174
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.400334130028
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.463878935462
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.449207320557
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.383569106538
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.399672923251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.42321390.35472646X-RAY DIFFRACTION96.23
2.84-2.870.39561420.34322707X-RAY DIFFRACTION96.41
2.87-2.910.35521380.30912608X-RAY DIFFRACTION96.59
2.91-2.950.31721430.27812731X-RAY DIFFRACTION96.64
2.95-30.33651390.2632624X-RAY DIFFRACTION95.77
3-3.040.31131380.25972638X-RAY DIFFRACTION95.1
3.04-3.090.29341360.24582567X-RAY DIFFRACTION93.4
3.09-3.150.27041430.23122728X-RAY DIFFRACTION97.39
3.15-3.210.29491410.22952670X-RAY DIFFRACTION97.13
3.21-3.270.28361420.23272712X-RAY DIFFRACTION97.14
3.27-3.330.26981400.22862657X-RAY DIFFRACTION96.65
3.33-3.410.25421420.2262699X-RAY DIFFRACTION96.76
3.41-3.490.25781410.21982673X-RAY DIFFRACTION96.97
3.49-3.570.24191410.19622668X-RAY DIFFRACTION96.7
3.57-3.670.21921420.18432700X-RAY DIFFRACTION96.24
3.67-3.780.22531410.17812677X-RAY DIFFRACTION96.77
3.78-3.90.2341400.17062659X-RAY DIFFRACTION96.12
3.9-4.040.22741390.17132654X-RAY DIFFRACTION95.32
4.04-4.20.20451380.16072620X-RAY DIFFRACTION94.68
4.2-4.390.17341360.1492584X-RAY DIFFRACTION93.66
4.39-4.620.17051360.1452573X-RAY DIFFRACTION92.05
4.62-4.910.17031390.14192644X-RAY DIFFRACTION95.37
4.91-5.290.2031390.14832651X-RAY DIFFRACTION94.26
5.29-5.820.23641380.16482611X-RAY DIFFRACTION94.02
5.82-6.660.22071360.17322596X-RAY DIFFRACTION93.21
6.66-8.390.19071350.16132559X-RAY DIFFRACTION91.45
8.39-64.790.19641320.17522541X-RAY DIFFRACTION89.49
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)
12.6332320769-1.11910105390.6321039140782.66669533634-2.11020011872.599730181820.2093725338990.326225097473-0.484553810223-0.285352940518-0.3052276127470.334826270740.5432224809240.465849519810.02124205434820.8720771352910.05206704701470.04119090961760.7267792072840.04282479831220.7092656054528.95616727120.250740522792.80865678731
22.24156560660.178994104563-0.5963349763811.88750230093-1.338011740733.362631238820.1013050121170.3778857734480.643652885499-0.181571351744-0.09531645306810.331844553768-0.910877227213-0.066004787828-0.06800015320120.689807500170.0662422721045-0.03975176938520.616921593942-0.04535709971980.686411461726-0.5579721617023.838987177456.18168153853
30.8996555202110.0598472431645-0.4913050405373.1616130089-0.1247069763474.202112499390.114117403566-0.1929450160270.166603980864-0.06615980177620.0362525914860.181265508028-0.48547232081-0.221442802637-0.1471650239510.762337090301-0.00427051242157-0.01494503242430.6041759401880.002658065409290.770675678028-6.2711696188811.01109556239.39726221378
43.08439007740.7401075686880.01095070518552.66227956887-0.8894719361212.364752619040.001063040247980.413051897940.183370338542-0.267311314927-0.09187582039760.353309023327-0.218673926691-0.5082121809530.07801681923230.8285891105960.177420506257-0.05434206453760.8409026259520.01209023811390.89586005367-19.021694444712.5028888037-0.704393308078
52.29117564477-0.2774898387261.018521313280.933489345251-1.4323958452.31826897361-0.09322716023940.431407758750.127907025254-0.139220211291-0.0963718627883-0.0111558744316-0.2163469542110.008440423765020.2277508773830.8532016405280.0449201732764-0.02943945559910.6529699436490.02579416215960.755965558549-5.5370487677418.8308156667-3.10958722191
62.53500574295-1.68113523142-0.5221502417552.796739890731.577123666842.487321781480.1549061045551.20276975050.592686559246-0.251566556567-0.631738725948-0.52788000352-0.310482766930.5686980222230.5817068463381.0304305371-0.009161253938780.07883508720421.050764310840.3063755501710.881931978423.4430407770720.2285562281-9.45548908778
78.10929152313-2.102115381844.403392679763.1254956719-0.2231821640462.71103415102-0.9227403772831.54982255550.4023038681150.02694594879530.120410785401-0.7889405118610.07000329831661.439288981460.3044678566370.7965724586190.2006309600680.2054722061010.9449421690810.104709476560.38403510262116.05718595452.7606520417-14.9891175196
87.35925003739-1.83273779596-0.3803865688835.548988651933.227237579034.99763028660.04263785560930.96526146321.82558700474-1.585741571070.457018710907-0.99256915488-1.066867045451.00124938698-0.3550319913260.791932399995-0.01964486380620.2289540668621.035590426760.3550796384970.81641818627217.247820060417.0867597875-9.62946432308
94.480837175180.507733757613-1.220724207653.31463475481-1.889095516592.947363628370.06439572325410.6296579607980.507326703946-0.894346399438-0.274264249733-0.438935879129-0.1346983444670.8191728767840.2080664897560.69561103253-0.0723254882916-0.002409679618870.8420502144260.1647332596160.71966714936915.620993611211.59108232280.963713031819
104.182265234192.882119294130.5895795656852.018440966970.1073420847653.6686723823-0.0194833503119-0.1905919203840.6240746872350.0886533869476-0.2677244140820.684647917551-0.670830456131-0.3163193546440.3376306849290.688084947350.05194697801330.1631447016980.738232116205-0.113777051330.791485520962-11.52524087792.5198888326730.7484147781
111.300193925950.181706212687-1.332378771892.485131121680.4846156100163.23652129736-0.01522895781030.142897555677-0.136771669037-0.7446611638040.111293280760.7285755449840.390527821658-0.204683962447-0.1334529169680.6270190446980.0294609580497-0.04517873337440.656364976385-0.01532865613330.86575723574-11.73166764740.36526277136820.4707134522
122.686597221371.863723095020.2152819982451.702474419540.551708157264.725878999810.09274927182150.0757970053017-0.349987040054-0.05984347170470.0306860371913-0.04491504167750.1007912718840.0331827639385-0.08375285238690.6760486118130.02912797000350.008907273894830.6037181107970.002764863600650.698542661883-11.8750602639-5.9397262722412.9574007457
131.553164221030.7625933197521.089194371663.83913405916-0.6456313169553.802724938880.01822053851870.0225849560510.150042930583-0.02496356543840.07338889804880.715557848091-0.162888739376-0.615752613796-0.1220711445830.648774786545-0.01215508605180.05953562849720.826818205775-0.01208329662360.809472890121-24.7259627708-4.050350676773.96363744477
143.081419271210.8654750256682.509489353991.168860916470.131179545756.06875597809-0.582378538313-0.520286694801-0.235281299976-0.0830356820160.00796635608340.7633483459980.433227761295-1.218675677680.371825106440.5929587341960.05133131599990.021057734840.743287316165-0.1176684550180.951897967797-27.5717910933-13.695746463118.3107157391
150.1544878372530.4920642969550.3510870596352.20030413280.3408882276621.413985184570.0372554588265-0.1957065225020.302326562153-0.0827009267387-0.07524118729340.245339626119-0.20055180451-0.294555703277-0.05080251919530.6722996752750.00924614185530.1365430389961.09184648937-0.248504314081.08679149123-23.0942876097-6.0232351061535.9635831485
161.32806246913-0.385328318488-0.3594610810691.827961403960.2943444701043.63742298245-0.378711217222-0.220136850416-0.03247581666970.171626990839-0.08237620836310.7345647164160.268695530754-1.018637997690.4006589554210.532716329888-0.04259048340630.1244133920741.1332720094-0.1667980587230.761636022825-26.8159795458-6.0300470848139.6372816427
175.592721959051.899999178691.055738030622.00521419429-0.9595703183834.337458685310.320560874416-0.9647866692680.3739788916850.555781133043-0.3374042010660.4389892126270.478536446626-0.5611102751230.03919062450450.645532075609-0.02579720329960.08797231853240.70896939626-0.05137908631520.584628428306-13.7698670306-9.2138397575936.2860869982
182.605449228-0.1566389935210.9939014417513.76654196082.721438360264.309087965570.139154069584-0.288119471076-0.09843856084810.534167384703-0.356135306285-0.1936885253310.256603816797-0.3007488941490.19703547760.744539168672-0.07278106842660.05000646785170.658013936720.03624331792080.5818195283317.199675663221.5087435269840.4908385482
193.02997918321.223540660080.0861112081772.692912814140.5376628997262.082828570580.1062814810830.3815434755640.1831546531920.199890063861-0.212390297829-0.139736960861-0.4629120922080.3955566188690.09765005064010.85403201996-0.0636550412623-0.007829204753460.6095834898240.005620796732190.79020783180721.01853265156.8979013991335.3100851845
201.89084697541-0.2387024751450.8541526533494.066957397830.7436929229042.57345504885-0.0747071660489-0.1667802966240.03614340681150.443201307109-0.093713019987-0.537160084901-0.1384356722110.3160495583920.1957651711570.852384732263-0.188876880206-0.05846569786880.7425480059650.09357613182980.87515242159232.64863751516.4763124611743.5178739035
213.034875657920.180423000329-2.273564246262.25743943789-0.3223679422752.49298091692-0.164401836353-0.6631218467710.2275416640140.5790646537140.033643375555-0.383743036628-0.1390951196910.07446240670280.2111374623521.08536460017-0.113539741323-0.03944433472480.722730035523-0.07276835048180.78656484220117.555901916816.935690572853.311518898
223.414640358030.85480234563-0.6419291713651.88261976495-0.1610916914934.957186011630.221538657376-0.8410993574480.3306694803440.269462741411-0.09924462966120.4310727996570.0568662497681-0.906475357043-0.05873122240061.0166041003-0.126077846790.07459799278670.875060525646-0.1232431728930.523280226864-0.950789003889.9164166591857.922152044
233.37724041570.4805362916170.3461229840652.62411764422.61427478342.805926825140.368117428424-0.3295059276180.3534818821640.718792203223-0.5219307393790.165941700282-0.235386151596-0.4017483527570.2461792531020.9707154078110.051981542816-0.05180989546490.711776437098-0.07505375491290.6909351854750.17559889752913.926880834443.702417393
243.02416587342-2.462451064340.6129412384823.330118009951.202387792323.613102323460.03620078719630.7549000206850.575530285468-0.193821431163-0.302771061674-0.575668924484-0.3820444144010.3348999378710.2807709342540.7058429672970.02112549732460.1120180360870.8746458262520.07462375463050.76379308168323.5873630045-2.5863674063813.6766365621
251.32146739958-0.866653627689-0.6479521678642.658599870370.6012381895871.494441049140.0365877383432-0.279002438735-0.006626712468590.447581602679-0.135042953422-0.2500378103390.1089705753110.5528509286520.09453899293510.621126473682-0.04912537196740.02159596597850.7680174361780.07314795458640.84668368017523.1035845982-4.7727228675424.1137512968
261.25882259913-1.038315447670.2412451675132.95149922094-0.4217277663314.135790964160.0284552541732-0.0125421578232-0.4243253458330.1187328091910.02749730769660.1170138525480.2633358844370.0126952841555-0.02997108139660.709012389826-0.015820764480.05561117443140.676516436002-0.01395609878990.74116404065221.2632714455-10.70765339231.5428336857
270.875212561280.0829258601070.1989839512032.00413044161-0.3006757187590.413342891950.2856718824950.581418015695-0.9253734049790.337213896165-0.53493172727-0.749827783278-0.1233328343910.8904445871070.4508371906090.957344004714-0.1651108099670.1284610833521.35417804290.205220948861.3714849277342.2230763532-3.3991573534333.2271532811
282.560982506381.147904207910.459005767221.667284452311.182121235992.726048495070.0987872291516-0.00620099021991-0.3918557452870.422346112768-0.303330982355-0.49367592068-0.05714729468670.533711655410.2102986962720.821173754132-0.00813921746012-0.03052930726130.8066650115990.1572606882040.88472916445231.6948527622-15.841745247843.4100409472
292.43102138419-0.9308191661821.492629643862.23381393550.1404986990231.968486981390.1408712323140.568807920744-0.104364491641-0.153024137524-0.282731623345-0.3504073151870.1411837286890.6190907569970.1444053787540.5953730658870.03913353457670.1077115641720.7704943336520.0578909416480.79832983849733.3414923551-21.957687675223.0879797271
303.22836860196-0.468096021957-0.8433521147474.5529700957-1.54956345253.750630274520.149175661950.5555539498960.00645031389042-0.484468885043-0.388345234479-1.248239846420.3348128137710.6301640832280.1791312325350.7017750089050.1499735442470.1180906711351.098647511490.1029476595910.89955451620836.5112580768-11.48170619833.87507366246
312.7998601016-1.72724179276-1.574803746342.793992171671.339418634333.665043881050.2165586387040.5582715997560.0186959752302-0.477420534905-0.350806922703-0.413841895465-0.01559821594060.4214209110850.08774007026170.5898455920070.05641907935150.0415738913040.893797407905-0.04779127607880.70533607604922.0838793266-14.69211120748.38162747439
323.22010533022-0.0239305358719-1.170116326820.606454781202-1.232915276695.111885885530.05009288163790.321454604722-0.2326094626250.08834219129070.1281974843090.6784595814970.0222148921309-0.639979723663-0.1404044784510.6426858607020.02907602044-0.01990399210740.8091960050320.07740904320140.972125890328-16.4799989324-48.596760231157.9826291055
330.04681693740040.295631224426-0.03599399532862.35088946113-1.014506618121.153298989050.396171467383-0.388555148650.1439312653030.2952551550760.3203533915180.546818148837-0.0277197680592-0.671653178241-0.6333787597680.7637444820630.1370284430320.2077490481421.361961685070.159219352371.31138958388-34.1623669889-46.502881306871.2381005165
342.327073852770.232200885665-0.2201087560331.63316477381-0.1595994814572.746456184390.1599574334540.570888553140.311113893306-0.1483419164350.03958056966880.645907996127-0.420525050633-0.967526427187-0.2100596778050.6259952040920.178832925769-0.0657166528520.9853295947020.1719706033061.00856658014-25.1350384108-40.326056738345.8533048463
352.294901297451.1916647289-0.6846562033382.42216259517-2.348766740844.280374717870.189032053015-0.1092795548970.1488193883880.308836984871-0.2091133605910.5382284158-0.440257062812-0.06970386529810.06434678917450.752463502551-0.1168446084660.08433647516050.698741678433-0.09918067570130.753258835588-5.24156106424-51.207153506379.4707597825
363.08484694985-1.113488836420.921050000494.82723738308-0.4135974845724.369648581-0.007942943942430.4498409499-0.2151805918520.3830150990550.09600137349030.2189719022810.38649470478-0.704321497607-0.1336927611340.716989752721-0.06886781694210.01609953154130.7859717626170.07693714805810.805034243582-14.7368716512-60.584593474871.2251883928
371.82697429026-0.934675595411-0.405376635691.36929181972-0.7125071998281.024625295310.120132050187-0.0949093418158-0.08970847797120.05092869924390.1663442832640.502048208116-0.0342696604644-0.872906754679-0.15008527790.800674601585-0.2463849207170.06810651541751.19875390840.05369499431361.07303146163-29.6886521324-62.965806809576.999840898
380.7493520138780.3714432463951.511107097271.759891040671.285538951183.000915711880.126741551315-0.163057048106-0.1053344767030.183905830962-0.0568046002980.141883738065-0.0870574810686-0.0363803926060.00744505242220.960483027165-0.2445585585880.0943575100270.875302560428-0.03546561238210.864345752694-9.9383411126-63.809856787591.5193626369
393.34997334478-0.8762535955160.008549934633262.05552534765-0.7946314575343.764243575010.379601987938-0.555250427166-0.6601971176770.68786641177-0.272138767436-0.06156931710950.1185098108320.000805920739116-0.06841165035070.864800763369-0.175201806686-0.07402306155380.6878793991180.0578265657380.8228863428973.65218402743-62.716411930688.9127459492
402.265435050731.178853551990.8913683199741.907074803241.683517806063.342801788170.251709337802-0.261392004414-0.144790314078-0.102953826914-0.281821911498-0.3828484461540.7514892163150.06450533991370.03509682005980.689753646292-0.06665647193550.04471824568330.5903193834270.008053720010060.71322708926514.9605211328-46.198913342675.4747525956
410.293104943074-0.000945954274228-0.1348813487242.13587034908-0.7733375448363.203847885030.274985023641-0.333647065703-0.276631285828-0.121810801469-0.01067511350140.0451519507916-0.1387503223570.527265412673-0.3002034870350.582041202457-0.04178014451-0.06892580550540.6200829895020.003562077303870.78071899481617.4187514178-43.861963743665.3794485275
422.020853657750.70805682196-0.7168192955270.806158576460.006248286653811.77419919037-0.09040930131490.124468357548-0.007189809845970.1991295207080.0862594829069-0.3889164194230.318265780110.2955641054850.0219122634190.7448425773630.0174682878011-0.03462199625910.728392393816-0.03199405960120.85457286829418.2088159778-37.958407917157.4933730911
431.45707328531-1.605953368340.3616061608772.898827489710.8532995603711.47191055428-0.164090617743-0.06713437749170.4035382549350.7271547579250.640135429711-1.04440484050.4300657792130.594990652732-0.5132215754320.935681239290.0876309506164-0.0911038820081.31637426394-0.06004151223761.0265311892138.4078168547-44.508799249462.1000567388
441.98460532102-0.981502772713-1.960083896561.849980296730.8657070961564.70510561833-0.1508619574010.148045648647-0.1514470435120.3818429945870.13707766755-0.523220237831-0.3454783660971.0254853937-0.0358247317340.76229441236-0.08183570281710.00719721034480.7201594801070.01903058202810.83952679752932.1750501793-31.7892675954.4259496485
450.653657422371-0.224897338049-1.320575324130.07199672980010.4660907943782.6066336630.08551082038670.1520263775530.0872048467879-0.153536777961-0.0692177489704-0.0810400040134-0.09790948273430.5361136922750.02333651727730.754857561957-0.0641311619698-0.01949731798120.665574492350.06628647036850.8581033045727.5780705927-29.947546215756.6465685265
460.774829403390.568758340757-0.01088098338820.79413990173-0.03617180463743.532680184710.196913294780.07159699308330.08020942220230.1937042014260.1209551338250.0726304437786-0.1793609396110.030814998627-0.2583411259850.826846411465-0.0571665224484-0.008865908410860.771170353971-0.01429967780150.79595393177926.2846398054-25.099022034574.6104730368
474.87223016311-0.688306779739-0.2275256788234.46318190227-0.3160629855491.123077146830.9402716257850.2684673982890.588212441021.16038694022-0.512472767654-0.4940425029590.646492590695-0.0577568504874-0.2118077129870.952202355056-0.0897283610253-0.3297694816450.7999853825860.1390147436330.71500362572826.6952078993-45.401771259191.4795598467
483.84228854225-0.6297343745940.8820721545045.04296408709-3.589424479065.13291407259-0.351222006417-0.0663215308160.635061450658-0.1621078399870.118679359653-0.996742204588-0.412873525988-0.02664848466130.2483587803570.839725223716-0.0859802476857-0.09299569269930.759418429625-0.08589961760080.7910689802322.8379162898-31.233298107386.3521965451
491.210097848260.412526047945-0.3368341165572.264903709731.700207090713.352045323710.351412338528-0.006982501769030.01547002192660.481794772556-0.368447255199-0.0568916469693-0.10349659648-0.2118808111110.03203214219130.813516123174-0.0887708591611-0.02052255451310.700519148082-0.0566372356090.83746171345911.6910692347-34.310192919780.2068649646
504.223247655810.422989413946-0.3792516703233.046714792962.823383476534.241129701740.175270286370.218450620460.669632954616-1.06760519951-0.222422761566-0.504306579056-0.710748385971-0.4700393353910.04552639822890.9038489482950.1227907865580.01803142622550.616998247723-0.03347410443160.7803735103673.71465973228-50.254853400343.100457669
513.18752681132-0.920609816449-0.2960395347741.803549399190.5666073930421.705106700240.0800106488606-0.102920737288-0.1710297706390.01019814373670.0489175276799-0.1747129121350.2611259883890.184961064071-0.1355630768980.7889385478880.01717433459070.0176054829720.6329308659790.03773999810820.82499676407416.4004400831-53.579762445352.1631594376
522.753466852341.30133403897-0.4905563171772.206279472820.2637261433851.93015453339-0.0589737090865-0.111281000456-0.424835176618-0.1879647730690.170974594438-0.695464266764-0.008047831569060.321120121219-0.08083150815930.8316926757040.1412755346270.05427439685720.8012530596920.01906499520710.88105477876932.3404051575-54.703459546749.5752980184
532.375913272820.9153306480120.2650107069892.679284422551.128658646983.59802407097-0.4009293145260.325450762543-0.278049142171-0.3786835098610.273983934188-0.623644915729-0.1709145006310.02873716431460.08190341888380.9387590689550.09245556987620.07361488865710.641512719524-0.009129686400270.77679497505317.2291245502-63.764047579434.344717957
543.919029909460.188787414049-0.8468158570464.26396328315-0.1566826783166.484380640030.1930465220271.24087665153-0.253783340573-1.044929144570.0160288338818-0.3946205890681.25033766496-0.19233231095-0.1783286388580.9749500771840.08656777760190.01135006681590.857046273236-0.0913274340620.7348355665686.13536296679-60.639271446826.9131463868
554.820942594950.56104120228-1.243016932162.420667335381.038259546122.531969380010.06553858286120.451091849471-0.564498559607-0.185887592913-0.09148746970.3546218808570.428086669787-0.578297436067-0.0174717688420.736114447509-0.0431971801472-0.09160690501910.574085703872-0.06521713265940.6962974363531.46242634694-62.963396680140.4212138057
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 40 )AA0 - 401 - 41
22chain 'A' and (resid 41 through 66 )AA41 - 6642 - 67
33chain 'A' and (resid 67 through 105 )AA67 - 10568 - 106
44chain 'A' and (resid 106 through 162 )AA106 - 162107 - 163
55chain 'A' and (resid 163 through 198 )AA163 - 198164 - 199
66chain 'A' and (resid 199 through 233 )AA199 - 233200 - 234
77chain 'A' and (resid 234 through 301 )AA234 - 301235 - 263
88chain 'A' and (resid 302 through 320 )AA302 - 320264 - 282
99chain 'A' and (resid 321 through 354 )AA321 - 354283 - 316
1010chain 'B' and (resid 0 through 40 )BB0 - 401 - 41
1111chain 'B' and (resid 41 through 66 )BB41 - 6642 - 67
1212chain 'B' and (resid 67 through 105 )BB67 - 10568 - 106
1313chain 'B' and (resid 106 through 162 )BB106 - 162107 - 163
1414chain 'B' and (resid 163 through 215 )BB163 - 215164 - 216
1515chain 'B' and (resid 216 through 245 )BB216 - 245217 - 246
1616chain 'B' and (resid 246 through 320 )BB246 - 320247 - 283
1717chain 'B' and (resid 321 through 354 )BB321 - 354284 - 317
1818chain 'C' and (resid 0 through 66 )CC0 - 661 - 67
1919chain 'C' and (resid 67 through 105 )CC67 - 10568 - 106
2020chain 'C' and (resid 106 through 171 )CC106 - 171107 - 172
2121chain 'C' and (resid 172 through 233 )CC172 - 233173 - 234
2222chain 'C' and (resid 234 through 320 )CC234 - 320235 - 287
2323chain 'C' and (resid 321 through 354 )CC321 - 354288 - 321
2424chain 'D' and (resid 0 through 40 )DD0 - 401 - 41
2525chain 'D' and (resid 41 through 66 )DD41 - 6642 - 67
2626chain 'D' and (resid 67 through 105 )DD67 - 10568 - 106
2727chain 'D' and (resid 106 through 122 )DD106 - 122107 - 123
2828chain 'D' and (resid 123 through 162 )DD123 - 162124 - 163
2929chain 'D' and (resid 163 through 233 )DD163 - 233164 - 234
3030chain 'D' and (resid 234 through 320 )DD234 - 320235 - 290
3131chain 'D' and (resid 321 through 354 )DD321 - 354291 - 324
3232chain 'E' and (resid 1 through 105 )EE1 - 1051 - 105
3333chain 'E' and (resid 106 through 162 )EE106 - 162106 - 162
3434chain 'E' and (resid 163 through 354 )EE163 - 354163 - 315
3535chain 'F' and (resid 0 through 66 )FF0 - 661 - 67
3636chain 'F' and (resid 67 through 105 )FF67 - 10568 - 106
3737chain 'F' and (resid 106 through 162 )FF106 - 162107 - 163
3838chain 'F' and (resid 163 through 301 )FF163 - 301164 - 268
3939chain 'F' and (resid 302 through 354 )FF302 - 354269 - 321
4040chain 'G' and (resid 0 through 40 )GG0 - 401 - 41
4141chain 'G' and (resid 41 through 66 )GG41 - 6642 - 67
4242chain 'G' and (resid 67 through 105 )GG67 - 10568 - 106
4343chain 'G' and (resid 106 through 122 )GG106 - 122107 - 123
4444chain 'G' and (resid 123 through 142 )GG123 - 142124 - 143
4545chain 'G' and (resid 143 through 198 )GG143 - 198144 - 199
4646chain 'G' and (resid 199 through 233 )GG199 - 233200 - 234
4747chain 'G' and (resid 234 through 283 )GG234 - 283235 - 256
4848chain 'G' and (resid 284 through 320 )GG284 - 320257 - 292
4949chain 'G' and (resid 321 through 354 )GG321 - 354293 - 326
5050chain 'H' and (resid 0 through 40 )HH0 - 401 - 41
5151chain 'H' and (resid 41 through 105 )HH41 - 10542 - 106
5252chain 'H' and (resid 106 through 171 )HH106 - 171107 - 172
5353chain 'H' and (resid 172 through 245 )HH172 - 245173 - 246
5454chain 'H' and (resid 246 through 320 )HH246 - 320247 - 286
5555chain 'H' and (resid 321 through 354 )HH321 - 354287 - 320

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  • 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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