[English] 日本語
Yorodumi
- PDB-7pd7: Crocagin methyl transferase CgnL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pd7
TitleCrocagin methyl transferase CgnL
ComponentsMethyltransferase
KeywordsBIOSYNTHETIC PROTEIN / RiPP / crocagin / CgnL / methyl transferase
Function / homologyS-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesChondromyces crocatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsZheng, D. / Koehnke, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101002326European Union
CitationJournal: Nat.Chem. / Year: 2023
Title: Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.
Authors: Adam, S. / Zheng, D. / Klein, A. / Volz, C. / Mullen, W. / Shirran, S.L. / Smith, B.O. / Kalinina, O.V. / Muller, R. / Koehnke, J.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Feb 28, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,20815
Polymers111,0264
Non-polymers2,18211
Water7,242402
1
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4175
Polymers27,7571
Non-polymers6614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3254
Polymers27,7571
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3254
Polymers27,7571
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1412
Polymers27,7571
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.947, 128.117, 94.295
Angle α, β, γ (deg.)90.000, 90.393, 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

-
Components

#1: Protein
Methyltransferase / Crocagin methyl transferase CgnL


Mass: 27756.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1EC20
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose, N-Acetyl-D-Glucosamine) 0.1 M Buffer System 1 (Imidazole, MES monohydrate) pH 6.5 37.5 % v/v Precipitant Mix 4 ...Details: 0.12 M Monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose, N-Acetyl-D-Glucosamine) 0.1 M Buffer System 1 (Imidazole, MES monohydrate) pH 6.5 37.5 % v/v Precipitant Mix 4 (12.5% each of MPD (v/v), PEG 1000 (w/v), PEG 3350 (w/v))

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.96→47.15 Å / Num. obs: 69598 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 1.96→2 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4446 / CC1/2: 0.519

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+23 / Resolution: 1.96→47.15 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 3542 5.09 %
Rwork0.1853 66010 -
obs0.1872 69552 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.25 Å2
Refinement stepCycle: LAST / Resolution: 1.96→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7619 0 146 402 8167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01187946
X-RAY DIFFRACTIONf_angle_d1.26410782
X-RAY DIFFRACTIONf_chiral_restr0.05211176
X-RAY DIFFRACTIONf_plane_restr0.00751420
X-RAY DIFFRACTIONf_dihedral_angle_d18.58581160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.35231200.29342619X-RAY DIFFRACTION99.89
1.99-2.020.31471430.27932656X-RAY DIFFRACTION99.86
2.02-2.050.26081250.26572662X-RAY DIFFRACTION99.89
2.05-2.080.30131280.25962622X-RAY DIFFRACTION99.93
2.08-2.110.3141550.2562609X-RAY DIFFRACTION99.93
2.11-2.150.30051900.24412637X-RAY DIFFRACTION100
2.15-2.190.29361610.22922570X-RAY DIFFRACTION99.96
2.19-2.230.27131250.23282634X-RAY DIFFRACTION100
2.23-2.270.25981600.21522688X-RAY DIFFRACTION99.96
2.27-2.320.26531340.21482577X-RAY DIFFRACTION100
2.32-2.380.26071370.20922645X-RAY DIFFRACTION99.93
2.38-2.440.2641300.20442635X-RAY DIFFRACTION100
2.44-2.50.25821580.20492623X-RAY DIFFRACTION100
2.5-2.580.27151410.19512653X-RAY DIFFRACTION99.96
2.58-2.660.23861560.18972598X-RAY DIFFRACTION100
2.66-2.760.18781750.18622630X-RAY DIFFRACTION100
2.76-2.870.23581440.17612634X-RAY DIFFRACTION99.96
2.87-30.22821280.18122651X-RAY DIFFRACTION100
3-3.150.191120.16542698X-RAY DIFFRACTION99.96
3.15-3.350.22381280.16652637X-RAY DIFFRACTION100
3.35-3.610.17691400.15952641X-RAY DIFFRACTION100
3.61-3.970.17451350.14472657X-RAY DIFFRACTION99.96
3.97-4.550.16791310.14282697X-RAY DIFFRACTION100
4.55-5.730.18231410.16132647X-RAY DIFFRACTION100
5.73-47.150.23991450.20912690X-RAY DIFFRACTION99.86
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)
12.840955686540.532013446287-0.2375491497431.981422035940.1542723507573.33101714822-0.06872489711220.403307969482-0.3485393093880.6349869879490.3560573399740.5168230997170.427396813991-0.0160105362043-0.02050972768570.4058917074380.0307457362358-0.0407200015430.412068855471-0.03527636613210.37670311631613.863457361234.971106892453.7943485851
24.06786605033-0.764804673996-0.5265858688313.346282140341.356611298865.628427172560.09191077569030.0264085055041-0.315418381279-0.2970300325590.0708185132757-0.251786779170.1949378374440.737701570739-0.009581626658860.3971771055310.06396288396740.07323136209250.2619256498060.03228521105280.47969168758423.55193146831.606928460772.6655030993
31.91223416874-0.141681941150.7981503540670.955415876881-0.5270744211893.77398355451-0.0520365522731-0.329488397212-0.3565205907110.3184511493090.1354535528210.3163541626940.1841298846920.017989093318-0.04564182373980.3419746121920.03318368079940.1029112744060.2324152678930.0818299430350.37621981067712.675262198233.020812246573.7724401808
42.66322959405-0.0199674100810.868534888111.31796108309-0.2015495500813.72268759032-0.0500134593858-0.0302551471507-0.1845630908480.09334527373490.06346282005540.245401895982-0.018703440114-0.410213075862-0.03705024120270.242250923090.02516606360980.04722926450.2574491515440.03131657789270.3202962497886.5158790057138.838367475168.6722352154
50.681052947997-0.495088046296-0.1971520012370.4693142613120.3414204112271.634597326330.0135030939901-0.07269135073010.0831968618779-0.007228619982470.129972867910.0814275181682-0.1031232865850.127746693626-0.04376957547460.2784843003390.01525790278680.001573933374720.2445236478110.01597827099170.287154931721.012081287844.989733224565.0085409743
61.155106281311.305342054980.0944729805861.942902463311.31248700632.300555734260.01834494907530.126376705902-0.2006724823640.2908922388190.470299910641-0.449230202071-0.1918818738690.198005750733-0.01139118261390.319086143056-0.00480774887936-0.01971709933570.2968638737490.03109390362260.26487619615222.72217927337.246662162548.2432238016
70.3521475707770.4048202613750.8939236153762.127659545411.886145363852.32464060484-0.04141501870640.03126584803960.107901249325-0.000671933181416-0.04324045981520.41283693742-0.00842598652175-0.00714673083471-0.005759472134170.2915791939-0.00402857938667-0.01654307455910.3058868075440.01512225546470.31401138193917.919354658139.418413984846.6434830813
81.63047150207-0.618352136398-0.3108904462222.171615507320.2367399572643.144156302720.044543919484-0.1092749781850.1222421202570.3106834497680.045934052359-0.0251044835141-0.5792770002610.367351131659-0.07550571136920.365766904757-0.0312056666492-0.002812238970040.281824691057-0.0159435804520.30074408895126.496660221551.35375153871.406983763
91.81738472351-0.471107908031-0.807599850441.622251289120.3325459917813.24102290283-0.352005360542-0.349570049271-0.5591433020990.201087762174-0.1276056062690.06554796129560.01349577515690.387554393126-0.07508025930220.2680476970330.01550513044040.005828875807840.3760884687510.03453373259230.32868437624129.379012605442.054079453272.210519461
103.6573469139-0.12986689822-0.1131040463082.65641313879-0.4259556154643.91136469940.2607252591480.46198199769-0.102635151458-0.167370631677-0.4803125683450.356173008888-0.220984223646-0.7877588540520.05315162095270.4569702377680.08808777938720.02882616175120.590107903589-0.07518449172510.351703529908-6.8114627593471.1541793476122.982642507
114.674297254240.0217912965139-1.494056351474.312977139171.674264331056.259533359070.0871326334285-0.1878338992820.7783645470960.2487705510.06184638340930.350181350771-1.19520193716-1.08862591811-0.02324018125010.5133663617830.135363401554-0.02070175166790.425220398453-0.03430177084070.454181893712-3.7320921034383.3337936428104.854833964
122.410388906460.668728415225-0.09392833074121.77838594436-0.3810049535623.68258617233-0.07365413878410.143951267649-0.0145806516704-0.1296248514480.01786974110250.3440385779420.13476048806-1.025147418850.03836797159940.202081341476-0.0367395749421-0.02269331848870.462864487389-0.08171123775480.259998302987-6.7179749899568.2110627637105.955296436
132.492223524310.2508590266680.4975096100182.10588014621-0.4971918741774.499179036080.0279052079504-0.02398914510480.0660510662621-0.0949200571101-0.1413501020080.01176338735450.0607852694111-0.2010888062780.1420813435820.199634425463-0.01657916144530.01287761202820.262585063182-0.03154114242720.2415274604897.0165326372869.7133701904106.805709644
142.538879013740.182063011995-2.373719046791.024736984741.147451181454.663607702790.30839267682-0.1536972269930.31337053132-0.03836354349350.26590691946-0.0882672143459-0.5487023671860.143720939431-0.4303107856140.349914378376-0.006553871993650.02841503979580.24410300167-0.004632707535730.3015664950354.2815808618383.2823299714125.651776096
151.75784545415-0.448248400179-2.528401656380.7690744357640.9991802347273.84249258560.03800787257060.07733170935760.04004492820210.03143438947640.0641693738253-0.06313716144240.02571208866790.17776829682-0.05841016343830.283689873927-0.00122704500944-0.04363980673880.238781193612-0.009786299622510.249361245789-0.87064442617474.4531305838130.220103788
161.79765399725-0.716405921888-1.86527821432.115813052511.20365185574.186173020310.0704894482154-0.05359388609470.0114865330253-0.06951522179940.222676395753-0.13674441543-0.4288279202950.784051415389-0.2665511326310.271750541986-0.08869021587720.03518937109910.324997549673-0.06065617637020.30906781648515.112345852175.4301748618106.939074817
171.323212231560.636585623481-1.802604156021.620096987830.06014672527435.29042809804-0.0291845373890.1934964212910.278487878055-0.864768237576-0.159824741670.179618530362-1.675762199570.185881299706-0.4153359748020.691623833619-0.0779700023585-0.004190139580610.33187193393-0.01916384368260.4092233263968.2296349579787.3492181229110.566378067
181.684375974890.179240250208-1.983290980310.4382981001531.083357441636.15195628496-0.08294690751670.2343199520210.330853851736-0.345758595949-0.3947387442460.277594656076-0.859301585644-0.594576573557-0.2566124346410.262801594289-0.06629478926110.03725602433020.319759494423-0.007645521537480.30185163014810.479810552774.719602923696.6503264557
194.287919635381.22720368476-0.5971022842164.727994718540.1090492182245.79194263337-0.1831323399540.3360622163210.4041902179340.4405827714780.0949853035594-0.123794200105-0.710722516607-0.00462896152521-0.008698240677230.378212741790.0228468602916-0.05624857664850.341047238389-0.0002848844688270.3333695400276.1309357993778.096912028656.2018951607
204.626381451550.214534819783-0.1339473169744.42262820015-1.315150503866.247295872720.1289863894490.05412495838180.8343525600950.03566088131880.136825692950.663320030097-0.785463526072-0.403629937697-0.04167553264630.4555619126960.0978850825517-0.03563109905160.306081939931-0.01884281572710.477105065458-4.8923706977282.301131600174.1722049865
212.450272759910.288484913804-1.030816082811.89117041050.1708877671555.27550546091-0.105138184875-0.3003996551710.3954065876850.2847975469370.0718184396205-0.403187306337-0.5579871099760.149237662124-0.05834126344830.3634166945730.00831255390345-0.0824931460010.328176498757-0.04912123122650.3911822309845.8883480026481.188321643475.9909517434
222.402551771040.56506590388-0.5847061849311.37067656976-0.4962657949933.11408963199-0.0657907744297-0.106758183589-0.01341812177580.1369953164670.00648587105199-0.232186549278-0.05137457272490.2683057923390.08312060190140.2342316610180.0448478251416-0.04102126808480.226705581432-0.01571255910180.2262056743537.1186226729270.745050953272.2922735104
231.065929009220.112272676391-0.336671191451.92062405219-1.574296156783.990304844990.0932475290559-0.03348380517680.198636380439-0.2347036889260.1999140583940.1908035589040.0709454832914-0.234604818274-0.1796877677690.2679565417840.0246793423423-0.0004038752479950.311180143202-0.04209584208330.277150955831-10.115481523174.460512715253.8441391648
240.9307016562840.616600367611-0.2157035873081.77635923335-1.676058532932.35804315230.0207077123513-0.05873179706530.0365206245416-0.1603816160740.02201034795430.2659634577490.24522170644-0.01383584727740.02598620218850.2493814143530.0125922386147-0.01304064044170.267701040811-0.01227477393130.245297202974-0.091172097838574.883882627949.4218999324
251.411280591030.05856983757090.5546330977291.75734298761-1.420584169283.84573714667-0.119064041058-0.0473718955365-0.2822820024520.1003554508550.1034493723260.1883970942670.697469224614-0.469843607273-0.02556767949760.29791676952-0.02205527436190.02635955416980.277573138835-0.006487289672090.2924806371-7.6405741681562.31850488973.1546224965
260.7314827956570.1941330126541.371269024740.492502738316-0.1659636872485.48831455842-0.304759523939-0.3907781445160.3322804686870.1649509840290.02610443525930.238008942984-0.381587498504-0.661082577273-0.120131694950.3374267429470.0463536860222-0.009460860992250.3966125041520.009770540255970.308400019316-10.700633908671.612702217273.6536885139
275.82232414044-3.68125963684-0.7936240951364.17185949462-0.1938807305882.866998982680.197337631499-0.101399644891-0.057419053345-0.0536500870706-0.1589626082040.002597986788870.5246568491290.40320734784-0.05664323256420.4803911309590.0148385305209-0.03449159844380.409339940880.04069316846230.32384863948125.952290133842.479546591121.451999152
285.0523186717-0.6397278676641.945996866553.60307791977-0.5313216125127.302647111580.0272200058897-0.168845917658-0.6658973895120.2472357028690.246117379962-0.2951668179740.7700208658050.4928910288630.02895057270.3633616660690.112094294862-0.009130938135540.2898361912380.03070636723710.42195013790922.841386893331.1681268844102.66944078
292.48507001778-0.0240109189476-0.5824076930641.944508290341.322581742865.502292083360.05183128320420.2813573500640.0825015561027-0.126060149525-0.0693425663102-0.2358437114370.08431655479230.56461448877-0.1059866865790.2151576775960.03055949545660.04398691831590.3841103698170.06569427465130.32025004984626.517221878241.9926360172102.140247193
305.23020247799-1.50367443525-2.403020089932.880221575740.5661434111296.393920145550.111439523397-0.175078306971-0.01135510035340.2404283923050.191284856299-0.580510236316-0.03934465421421.59489208572-0.2476353560580.223835339826-0.0891998629442-0.0476608350110.5364071835670.0354197619610.3919746362832.22665290146.4171065765112.427249188
312.027804344490.3588879615540.2822838648421.683588028721.160703840114.556797700130.1529105245910.4092662661770.620293316153-0.067182382432-0.158873250159-0.0427670809521-0.4859737942560.70881796094-0.1113116566040.296631936703-0.009957467750060.0715271976110.3342161056380.1207299307270.35952586625921.715089245551.7180707621103.545989236
322.31485173621-0.301930607837-1.213764558741.201984092540.7235657135434.579136571150.1823527626840.1431699169530.144769720885-0.0288253814545-0.0782394786068-0.0734766228092-0.115527954359-0.0828171603555-0.002600645283650.2309540346950.009035414023170.007435464590880.2488873519340.06439659913740.2703160869312.167979179244.731745691105.321896389
333.01699267006-0.2193174860511.985041903620.651346175717-0.6076842991194.106336056840.342290643561-0.0978901639933-0.324534580746-0.07097651076250.1818030127160.08096999103310.45788727596-0.106650466693-0.3579950974590.384014189462-0.0334982560746-0.03401280084320.297351290837-0.001415085526610.29310835738814.791149358630.2082074714123.636991547
342.36598604074-0.7697849375141.982005165371.11093603-1.092614658013.530956192620.2328036287580.0429863456907-0.367164347779-0.008255876727330.1140388991270.1339474204010.063816703413-0.161322228261-0.1071975914190.346896156448-0.03519782769260.02169286058030.2455318058480.0196216936790.27020928487219.808866678136.2749058764127.561279478
352.16372784708-0.8094416101492.481843239650.311596942827-0.8736313479782.90641033073-0.232708710165-0.004118816165060.2750711665170.04815514174940.0652932282548-0.00575138783654-0.161876292822-0.0124120018430.02362936120250.281557449861-0.0221075732333-0.005462061109930.2339892816950.00179288662220.25361679389220.178497739441.3418911912129.317007163
362.52207861061-1.260083174541.654534134272.13005081795-1.217104316513.563143147430.2327605167550.228792699539-0.0133530606234-0.121918239905-0.1264222614620.1941788485310.182184943947-0.627360842356-0.1299913320910.24971052822-0.0443326984536-0.03384595297450.3675126688470.04582782074770.285091608973.9697847028139.1161072896105.149069218
372.09635942445-1.180271401012.125370982710.660894570637-1.006277093413.16448704185-0.1218547270940.396631134309-0.271811633979-0.355675147788-0.331166476852-0.5139847552440.986932689437-0.206274517266-0.1768979756330.46042062026-0.03380583932260.01840568876560.352314360346-0.01205675184290.28034945110710.281078196432.2297140103103.169655095
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 17 )AA-1 - 171 - 19
22chain 'A' and (resid 18 through 35 )AA18 - 3520 - 37
33chain 'A' and (resid 36 through 58 )AA36 - 5838 - 60
44chain 'A' and (resid 59 through 99 )AA59 - 9961 - 101
55chain 'A' and (resid 100 through 153 )AA100 - 153102 - 155
66chain 'A' and (resid 154 through 177 )AA154 - 177156 - 179
77chain 'A' and (resid 178 through 201 )AA178 - 201180 - 203
88chain 'A' and (resid 202 through 223 )AA202 - 223204 - 225
99chain 'A' and (resid 224 through 245 )AA224 - 245226 - 247
1010chain 'B' and (resid -2 through 17 )BE-2 - 171 - 20
1111chain 'B' and (resid 18 through 35 )BE18 - 3521 - 38
1212chain 'B' and (resid 36 through 99 )BE36 - 9939 - 102
1313chain 'B' and (resid 100 through 137 )BE100 - 137103 - 140
1414chain 'B' and (resid 138 through 153 )BE138 - 153141 - 156
1515chain 'B' and (resid 154 through 201 )BE154 - 201157 - 204
1616chain 'B' and (resid 202 through 223 )BE202 - 223205 - 226
1717chain 'B' and (resid 224 through 237 )BE224 - 237227 - 240
1818chain 'B' and (resid 238 through 247 )BE238 - 247241 - 250
1919chain 'C' and (resid -2 through 17 )CG-2 - 171 - 20
2020chain 'C' and (resid 18 through 35 )CG18 - 3521 - 38
2121chain 'C' and (resid 36 through 58 )CG36 - 5839 - 61
2222chain 'C' and (resid 59 through 137 )CG59 - 13762 - 140
2323chain 'C' and (resid 138 through 153 )CG138 - 153141 - 156
2424chain 'C' and (resid 154 through 201 )CG154 - 201157 - 204
2525chain 'C' and (resid 202 through 223 )CG202 - 223205 - 226
2626chain 'C' and (resid 224 through 245 )CG224 - 245227 - 248
2727chain 'D' and (resid -2 through 17 )DJ-2 - 171 - 20
2828chain 'D' and (resid 18 through 35 )DJ18 - 3521 - 38
2929chain 'D' and (resid 36 through 68 )DJ36 - 6839 - 71
3030chain 'D' and (resid 69 through 79 )DJ69 - 7972 - 82
3131chain 'D' and (resid 80 through 99 )DJ80 - 9983 - 102
3232chain 'D' and (resid 100 through 137 )DJ100 - 137103 - 140
3333chain 'D' and (resid 138 through 153 )DJ138 - 153141 - 156
3434chain 'D' and (resid 154 through 177 )DJ154 - 177157 - 180
3535chain 'D' and (resid 178 through 201 )DJ178 - 201181 - 204
3636chain 'D' and (resid 202 through 223 )DJ202 - 223205 - 226
3737chain 'D' and (resid 224 through 246 )DJ224 - 246227 - 249

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more