[English] 日本語
Yorodumi
- PDB-8pha: O(S)-methyltransferase from Pleurotus sapidus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pha
TitleO(S)-methyltransferase from Pleurotus sapidus
ComponentsO-methyltransferase domain-containing protein
KeywordsTRANSFERASE / biocatalysis / enzymes / fungi / O-methyltransferase / Pleurotus sapidus / S-methyltransferase
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
2-HYDROXY BUTANE-1,4-DIOL / L-ornithine / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesPleurotus sapidus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKorf, L. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0307B Germany
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: A Novel O - and S -Methyltransferase from Pleurotus sapidus Is Involved in Flavor Formation.
Authors: Brescia, F.F. / Korf, L. / Essen, L.O. / Zorn, H. / Ruehl, M.
History
DepositionJun 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-methyltransferase domain-containing protein
B: O-methyltransferase domain-containing protein
C: O-methyltransferase domain-containing protein
D: O-methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,68718
Polymers214,5684
Non-polymers1,11914
Water21,8881215
1
A: O-methyltransferase domain-containing protein
C: O-methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8449
Polymers107,2842
Non-polymers5607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O-methyltransferase domain-containing protein
D: O-methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8449
Polymers107,2842
Non-polymers5607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.363, 109.116, 192.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 22 or resid 24...
d_2ens_1(chain "B" and (resid 6 through 22 or resid 24...
d_1ens_2(chain "C" and (resid -1 through 13 or resid 15...
d_2ens_2(chain "D" and (resid -1 through 13 or resid 15...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROTHRA1 - 17
d_12ens_1ALATHRA19 - 37
d_13ens_1GLYLEUA39 - 51
d_14ens_1LEULYSA53 - 54
d_15ens_1LEULEUA57 - 103
d_16ens_1LYSPROA105 - 107
d_17ens_1GLYVALA109 - 142
d_18ens_1SERPHEA144 - 235
d_19ens_1VALLEUA237 - 241
d_110ens_1ASNALAA243 - 305
d_111ens_1ARGASPA310 - 341
d_112ens_1ASPALAA343 - 368
d_113ens_1HISALAA370 - 450
d_21ens_1PROTHRB1 - 17
d_22ens_1ALATHRB19 - 37
d_23ens_1GLYLEUB39 - 51
d_24ens_1LEULYSB53 - 54
d_25ens_1LEULEUB57 - 103
d_26ens_1LYSPROB105 - 107
d_27ens_1GLYVALB109 - 142
d_28ens_1SERPHEB144 - 235
d_29ens_1VALLEUB237 - 241
d_210ens_1ASNALAB243 - 305
d_211ens_1ARGASPB310 - 341
d_212ens_1ASPALAB343 - 368
d_213ens_1HISALAB370 - 450
d_11ens_2ARGILEC1 - 15
d_12ens_2ALATHRC17 - 24
d_13ens_2ALAGLUC26 - 27
d_14ens_2ALAASPC29 - 34
d_15ens_2GLNLEUC36 - 58
d_16ens_2LEUASNC60 - 62
d_17ens_2LEUMETC64 - 85
d_18ens_2ASNPROC87 - 114
d_19ens_2GLYARGC116 - 214
d_110ens_2GLYGLYC216 - 219
d_111ens_2LEUTRPC221 - 257
d_112ens_2GLUHISC259 - 286
d_113ens_2VALALAC289 - 312
d_114ens_2ARGTHRC317 - 381
d_115ens_2ILELEUC383 - 426
d_116ens_2ASPVALC428 - 451
d_117ens_2GLUALAC453 - 457
d_21ens_2ARGILED1 - 15
d_22ens_2ALATHRD17 - 24
d_23ens_2ALAGLUD26 - 27
d_24ens_2ALAASPD29 - 34
d_25ens_2GLNLEUD36 - 58
d_26ens_2LEUASND60 - 62
d_27ens_2LEUMETD64 - 85
d_28ens_2ASNPROD87 - 114
d_29ens_2GLYARGD116 - 214
d_210ens_2GLYGLYD216 - 219
d_211ens_2LEUTRPD221 - 257
d_212ens_2GLUHISD259 - 286
d_213ens_2VALALAD289 - 312
d_214ens_2ARGTHRD317 - 381
d_215ens_2ILELEUD383 - 426
d_216ens_2ASPVALD428 - 451
d_217ens_2GLUALAD453 - 457

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999467625124, -0.0317302062675, -0.00759344048083), (-0.031675526446, 0.999472155684, -0.00721602639907), (0.00781839833251, -0.00697165854315, -0.999945132807)49.5873526324, -0.813133502384, 96.5347506934
2given(-0.999176066836, -0.037104454399, -0.0164452706236), (-0.0370178990548, 0.999299263644, -0.00553686107135), (0.0166391890337, -0.00492352970001, -0.999849436787)50.290993975, -0.894957564681, 96.477149106

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
O-methyltransferase domain-containing protein


Mass: 53642.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus sapidus (fungus) / Gene: PLEOSDRAFT_1114007 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067NAT9

-
Non-polymers , 5 types, 1229 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9O3
#4: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1215 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15%(w/v) PEG 3K, 20%(v/v) 1,2,4-butanetriol, 1%(w/v) NDSB 256 0.01 M of each Polyamine 0.1 M GlyGly/AMPD. AMPD: 2-amino-2-methyl-1,3-propanediol; NDSB 256 Surfactant (PDB ID: DMX) Polyamine: ...Details: 15%(w/v) PEG 3K, 20%(v/v) 1,2,4-butanetriol, 1%(w/v) NDSB 256 0.01 M of each Polyamine 0.1 M GlyGly/AMPD. AMPD: 2-amino-2-methyl-1,3-propanediol; NDSB 256 Surfactant (PDB ID: DMX) Polyamine: Spermine 4 HCl (PDB ID: SPM), Sermidine 3 HCl (PDB ID: SPD), 1,4Diaminobutane 2 HCl (PDB ID:PUT), DL-Ornithine HCl (PDB ID:ORD/ORN)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.02→48.23 Å / Num. obs: 119562 / % possible obs: 96.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 30.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.042 / Rrim(I) all: 0.101 / Net I/σ(I): 9.5
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5979 / CC1/2: 0.715 / Rpim(I) all: 0.395 / Rrim(I) all: 0.978

-
Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→48.23 Å / SU ML: 0.2018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 5948 4.98 %
Rwork0.1707 113377 -
obs0.1728 119325 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.62 Å2
Refinement stepCycle: LAST / Resolution: 2.02→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14167 0 72 1215 15454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005714760
X-RAY DIFFRACTIONf_angle_d0.769920131
X-RAY DIFFRACTIONf_chiral_restr0.04822299
X-RAY DIFFRACTIONf_plane_restr0.00692615
X-RAY DIFFRACTIONf_dihedral_angle_d14.23685524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.380929829297
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.449593703087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.24951000.23141641X-RAY DIFFRACTION39.42
2.04-2.070.27991260.22452017X-RAY DIFFRACTION48.14
2.07-2.090.28911200.22772306X-RAY DIFFRACTION54.3
2.09-2.120.28771230.21872636X-RAY DIFFRACTION61.64
2.12-2.150.25821350.21972877X-RAY DIFFRACTION68.21
2.15-2.180.25841790.21963037X-RAY DIFFRACTION72.35
2.18-2.210.28051590.21543300X-RAY DIFFRACTION77.63
2.21-2.240.24241970.21193493X-RAY DIFFRACTION82.98
2.24-2.280.27912020.21413711X-RAY DIFFRACTION87.36
2.28-2.310.24282010.2053925X-RAY DIFFRACTION93.69
2.31-2.350.25882200.19564138X-RAY DIFFRACTION97.19
2.35-2.40.23331990.18594168X-RAY DIFFRACTION97.7
2.4-2.440.21992310.19934156X-RAY DIFFRACTION97.92
2.44-2.490.24962220.18284138X-RAY DIFFRACTION97.98
2.49-2.550.23472200.17474052X-RAY DIFFRACTION95.42
2.55-2.60.24422350.17244200X-RAY DIFFRACTION99
2.6-2.670.22592040.16634216X-RAY DIFFRACTION99.26
2.67-2.740.22312080.1624247X-RAY DIFFRACTION99.31
2.74-2.820.20872340.15254223X-RAY DIFFRACTION99.35
2.82-2.910.20412220.15714231X-RAY DIFFRACTION99.26
2.91-3.020.2112260.15574246X-RAY DIFFRACTION99.6
3.02-3.140.20132190.154286X-RAY DIFFRACTION99.62
3.14-3.280.17582220.15094237X-RAY DIFFRACTION99.58
3.28-3.450.18452100.14974244X-RAY DIFFRACTION98.63
3.45-3.670.20082110.16914132X-RAY DIFFRACTION96.06
3.67-3.950.18362480.14494231X-RAY DIFFRACTION98.83
3.95-4.350.1792320.14684303X-RAY DIFFRACTION99.5
4.35-4.980.1722100.1494329X-RAY DIFFRACTION99.1
4.98-6.270.25612110.19584363X-RAY DIFFRACTION98.94
6.27-48.230.21022220.18564294X-RAY DIFFRACTION93.48
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8487247515240.147111173746-0.2795156348570.6058901369060.0306397583610.5043019017220.27282025845-0.2630072673790.5550088986890.376602155151-0.08864747976880.48390824061-0.162684085308-0.1347353156510.09589145711670.337323722282-0.1226570264780.1130909978040.261355490043-0.02051127021660.31615593546649.84265835282.682645843761.3381962319
20.2689565525010.0220298530752-0.2025820191610.1361223690530.1230424699390.4005074059230.0871367927448-0.01535781638790.07087043536070.0386689412515-0.0786314535907-0.03715413641260.04738397744860.00163815686707-0.00121511011950.227712297199-0.0407587616310.006490814964280.1903973754430.01332830931630.24884700165761.13929607515.6328009852444.347077086
30.4206976751290.05145449996050.3279396631760.855053319031-0.1169636037451.025664752920.0593500154468-0.07329500807880.02315734981520.181683417584-0.08521409022640.08490334168050.07758996923160.03230392714690.0002054213333590.173121747492-0.01974670351110.05248346166330.181562133948-0.01167236444830.190785794819-11.281090839310.570874605174.3087256188
40.420778836551-0.3454815149830.08436399108590.864179751143-0.1549673551560.7022708731550.0690539308704-0.09096084870360.2446398888140.114027623426-0.079818424793-0.0463395256698-0.3270399078530.117804466848-0.02511601994910.293406485272-0.1004910692280.05373767228960.233247772348-0.009488481540320.256615043015-0.72313399001629.408095247373.3984899498
50.8696006591170.5175453247820.01066637688080.810592890487-0.3954989905181.924957791410.160238744448-0.02642202154790.3156765451770.440020151828-0.173814251944-0.0126248731708-0.5586315947760.258748245093-0.02130764547270.533952968791-0.1663124963610.02918538349930.241376451278-0.01812593216310.2695829668411.1192487171125.425670093697.9745629863
60.6300895833320.007929970875620.2325366476180.7376455114070.1005530768621.449184587440.0435663754370.09943541899640.0380128976152-0.0707460272085-0.0602129106494-0.1213517641750.134208372948-0.0400491540814-0.00863165906760.1625558007120.01538561766330.0390384281670.1433600593240.02319448879690.20631807396859.72211492419.4443852723722.2121426214
70.902560152317-0.2494844909650.6425939186850.3511371770910.1487596943262.93335034406-0.03642169036070.09531367638890.231473186598-0.214061184404-0.05952113207860.018447626664-0.633684228479-0.24521849364-0.1946946215820.4089696011940.1057649345180.01308132974820.2163434533610.04105875509190.21486144987346.532193725623.940783743-1.57884133613
80.581993767260.407860306586-0.4327546302550.8963539140610.2187844387011.01282647088-0.08577306671430.03276682413780.3138588556080.02255738181090.0250228427153-0.0458478931626-0.621548434791-0.308239301471-0.07191495511410.2722534118790.1686261475580.06148926630640.2132543529130.02925419781780.2347713152348.798872844728.116232189822.9575441258
90.0649640667002-0.005669828912440.09345278387180.0143944983419-0.002658613480660.123199993460.04787744881340.0333454385636-0.370335908731-0.0141338972782-0.06108219693230.3422155751520.422387246533-0.01151743121520.004866401699250.322541150857-0.02869095225180.01530997292840.25771703513-0.007321466592090.269108588708-11.0904134819-6.3814890403173.3540655867
100.1479579479490.245618338381-0.09398144822050.5539909283570.04115266533490.887736365910.0710992548051-0.000934675045618-0.0730358660950.0649713651697-0.0781211922214-0.1438241572230.1448874000160.325479680009-0.003801591271620.1808884590640.030624386967-0.005195745612810.3326164637360.0409894824350.2495440519267.78170926917.2471720083872.9100900028
110.1527025482440.0218691209871-0.1591421215430.6313356255850.2055752110490.3476465983240.07415784461560.1185577616810.072457431139-0.0709358614404-0.177838311094-0.239130151324-0.009132551206730.4029918028250.00177369110020.198719073465-0.02465279239150.03204458640020.3222418137850.03836151394640.2273099277066.9979405661918.863561072662.350428477
120.09802566081420.0372522207678-0.04890948689930.04373153181190.01303944437720.03393199780080.2991076328020.1037084231450.0684214158921-0.36037591223-0.474036665347-0.43464563593-0.1089663414510.323352449358-0.01000546815170.2801659521630.02680759303460.1350094338290.4088785032740.06664380240620.39582280261911.58901231918.26699267650.5526787075
130.310390833343-0.3668331276690.07614088209450.3954864375990.0704586574310.3529447952730.179084674055-0.01262307806130.0452543624092-0.0430917441935-0.13493034106-0.326413203927-0.1764452462190.1148543229370.02506804870560.2756706484530.04254331399290.07962089017230.24020397609-0.0004496397620080.3140313923246.458023788-3.4569686946340.6952034656
140.678440231039-0.204603584944-0.190958478150.7141680250640.07066612987870.3009349691030.2061129545810.3856908663660.391991456949-0.509371417464-0.14556304195-0.474895421867-0.2437795849920.0682434397893-0.02193047810090.3868377730610.1297764535140.1144220616370.3089766729810.04480152091930.277272953689-0.6672331664153.7429746001735.1678489532
150.293632462111-0.0324959468147-0.2038391250020.165287448732-0.1089035704920.1929912693730.1351520512390.114890314750.0575227858606-0.0377901253863-0.09943988639250.05207797620260.06536510229850.0697090707343-0.0004770987976370.2178213459420.03896088330010.01256982291810.235283282751-0.001890098305010.223560183538-12.14795787426.4233286258452.039853017
160.5650856409480.2892383999240.4230751276890.367444579551-0.02707392111170.7664595610730.2784358111-0.148639143433-0.377375657050.0965917429616-0.10207754168-0.4288210624460.8005415711660.1815640026750.4200578440990.4292452345510.0138900345177-0.00938422459780.1448143644430.04459627762710.22416125216560.3857330061-7.2890897254123.0469751187
170.36703714784-0.328947818429-0.2220037392170.544618923759-0.08702710407111.301575754540.06260966990520.0417658858124-0.0731935973878-0.000747933181148-0.04351058880950.04361398132890.208688048743-0.3795585679510.03508723365280.160552309769-0.06645356126040.01539915973260.276422664884-0.01012153606890.18972693200741.216203025.4174456584823.7998903447
180.2642116870920.159696082349-0.07504528383570.527550800081-0.271298561350.2677882731990.00419634601165-0.05677557059170.05543269059680.0428914900433-0.1132151164490.149662368432-0.110564161163-0.475485026673-0.001111593318340.1937069548940.01598776076370.02875598030780.30988552305-0.03291041089130.21433852194741.398551799817.160542037633.8809814576
190.267866113224-0.1698087852670.2097371828580.303336974044-0.1024277296460.2869176517960.244498204174-0.287781633325-0.09758399996170.191320818227-0.307489087910.518597666706-0.00445898132344-0.3930253341530.04327135320520.271670622216-0.03306831660490.09047613812020.461339054162-0.03184513350030.33334257181337.139405032616.541466483545.9468194168
200.3247529933270.2194121493980.08288854413480.284173718903-0.2331495649010.3767460602960.1240835491030.06868822430940.0256732206643-0.0530726759391-0.07547959602720.3935623686370.0375860765739-0.1661923955550.0009211125115220.266973426806-0.06585452847210.05332266918570.2308385719860.01766910147880.32575119299742.8331265903-4.5866987745656.0133677768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 307 through 370 )BB307 - 370302 - 365
22chain 'B' and (resid 371 through 455 )BB371 - 455366 - 450
33chain 'C' and (resid -1 through 140 )CC-1 - 1401 - 142
44chain 'C' and (resid 141 through 243 )CC141 - 243143 - 245
55chain 'C' and (resid 244 through 455 )CC244 - 455246 - 457
66chain 'D' and (resid -1 through 140 )DD-1 - 1401 - 142
77chain 'D' and (resid 244 through 455 )DD244 - 455246 - 457
88chain 'D' and (resid 141 through 243)DD141 - 243143 - 245
99chain 'A' and (resid 6 through 34 )AA6 - 341 - 29
1010chain 'A' and (resid 35 through 140 )AA35 - 14030 - 135
1111chain 'A' and (resid 141 through 213 )AA141 - 213136 - 208
1212chain 'A' and (resid 214 through 243 )AA214 - 243209 - 238
1313chain 'A' and (resid 244 through 306 )AA244 - 306239 - 301
1414chain 'A' and (resid 307 through 370 )AA307 - 370302 - 365
1515chain 'A' and (resid 371 through 455 )AA371 - 455366 - 450
1616chain 'B' and (resid 6 through 34 )BB6 - 341 - 29
1717chain 'B' and (resid 35 through 140 )BB35 - 14030 - 135
1818chain 'B' and (resid 141 through 213 )BB141 - 213136 - 208
1919chain 'B' and (resid 214 through 243 )BB214 - 243209 - 238
2020chain 'B' and (resid 244 through 306 )BB244 - 306239 - 301

+
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://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