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- PDB-9enh: L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindr... -

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Basic information

Entry
Database: PDB / ID: 9enh
TitleL-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindrosporum
ComponentsL-amino acid oxidase 4
KeywordsOXIDOREDUCTASE / L-AMINO ACID OXIDASE / FAD / FLAVOPROTEIN
Function / homology
Function and homology information


L-arginine oxidase / L-glutamate oxidase / Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / L-lysine oxidase / L-amino-acid oxidase / L-amino-acid oxidase activity / amino acid catabolic process / extracellular region
Similarity search - Function
: / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / S-1,2-PROPANEDIOL / L-amino-acid oxidase 4
Similarity search - Component
Biological speciesHebeloma cylindrosporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGilzer, D. / Koopmeiners, S. / Fischer von Mollard, G. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2024
Title: Crystal structure and enzyme engineering of the broad substrate spectrum l-amino acid oxidase 4 from the fungus Hebeloma cylindrosporum.
Authors: Koopmeiners, S. / Gilzer, D. / Widmann, C. / Berelsmann, N. / Spross, J. / Niemann, H.H. / Fischer von Mollard, G.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-amino acid oxidase 4
B: L-amino acid oxidase 4
C: L-amino acid oxidase 4
D: L-amino acid oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,31533
Polymers248,7914
Non-polymers5,52429
Water2,162120
1
A: L-amino acid oxidase 4
B: L-amino acid oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,58021
Polymers124,3952
Non-polymers3,18419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: L-amino acid oxidase 4
D: L-amino acid oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,73512
Polymers124,3952
Non-polymers2,34010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.636, 158.283, 217.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 66 through 90 or resid 92...
d_2ens_1(chain "B" and (resid 66 through 90 or resid 92...
d_3ens_1(chain "C" and (resid 66 through 90 or resid 92...
d_4ens_1(chain "D" and (resid 66 through 90 or resid 92...

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_11ARGARGPHEPHEAA66 - 9013 - 37
d_12ILEILEALAALAAA92 - 12139 - 68
d_13ARGARGSERSERAA123 - 12970 - 76
d_14ASNASNILEILEAA134 - 19281 - 139
d_15SERSERVALVALAA194 - 295141 - 242
d_16GLUGLUPHEPHEAA299 - 319246 - 266
d_17PHEPHECYSCYSAA328 - 458275 - 405
d_18THRTHRTHRTHRAA460 - 495407 - 442
d_19TYRTYRASNASNAA497 - 513444 - 460
d_110ASNASNPHEPHEAA515 - 597462 - 544
d_111FADFADFADFADAE701
d_21ARGARGPHEPHEBB66 - 9013 - 37
d_22ILEILEALAALABB92 - 12139 - 68
d_23ARGARGSERSERBB123 - 12970 - 76
d_24ASNASNILEILEBB134 - 19281 - 139
d_25SERSERPHEPHEBB194 - 319141 - 266
d_26PHEPHECYSCYSBB328 - 458275 - 405
d_27THRTHRTHRTHRBB460 - 495407 - 442
d_28TYRTYRASNASNBB497 - 513444 - 460
d_29ASNASNPHEPHEBB515 - 597462 - 544
d_210FADFADFADFADBO701
d_31ARGARGPHEPHECC66 - 9013 - 37
d_32ILEILEALAALACC92 - 12139 - 68
d_33ARGARGSERSERCC123 - 12970 - 76
d_34ASNASNILEILECC134 - 19281 - 139
d_35SERSERVALVALCC194 - 295141 - 242
d_36GLUGLUPHEPHECC299 - 319246 - 266
d_37PHEPHECYSCYSCC328 - 458275 - 405
d_38THRTHRTHRTHRCC460 - 495407 - 442
d_39TYRTYRASNASNCC497 - 513444 - 460
d_310ASNASNPHEPHECC515 - 597462 - 544
d_311FADFADFADFADCX701
d_41ARGARGPHEPHEDD66 - 9013 - 37
d_42ILEILEALAALADD92 - 12139 - 68
d_43ARGARGILEILEDD123 - 19270 - 139
d_44SERSERVALVALDD194 - 295141 - 242
d_45GLUGLUCYSCYSDD299 - 458246 - 405
d_46THRTHRTHRTHRDD460 - 495407 - 442
d_47TYRTYRASNASNDD497 - 513444 - 460
d_48ASNASNPHEPHEDD515 - 597462 - 544
d_49FADFADFADFADDCA701

NCS oper:
IDCodeMatrixVector
1given(-0.957283646532, -0.00245981826045, 0.289140051492), (0.00473120017439, -0.999963195933, 0.00715699127672), (0.289111805064, 0.00821925016962, 0.957260052493)92.31501108, 68.7320118265, -13.8300231849
2given(0.129631622903, -0.991533580281, -0.00753667825135), (0.99025998794, 0.129068216877, 0.0522163928029), (-0.0508015612821, -0.0142321666555, 0.99860735367)61.7127440963, -0.125223917135, -53.1149151386
3given(-0.136215882641, 0.99001933743, 0.0361516919542), (-0.931141835567, -0.140404251439, 0.336543501251), (0.338260425372, 0.0121802172649, 0.940973712138)6.39215641574, 99.635866148, -72.298594651

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Components

#1: Protein
L-amino acid oxidase 4


Mass: 62197.676 Da / Num. of mol.: 4 / Mutation: K474A, K475A
Source method: isolated from a genetically manipulated source
Details: residues 54 - 615 obtained by limited proteolysis; surface entropy reduction mutations K474A and K475A
Source: (gene. exp.) Hebeloma cylindrosporum (fungus) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: S4S6Z0, L-amino-acid oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein: 10 mg/ml; reservoir solution: 2.25 M (NH4)2SO4, 0.1 M sodium citrate, pH 6.5; drop with 200 nl protein + 100 nl reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.3→49.6 Å / Num. obs: 84158 / % possible obs: 70.5 % / Redundancy: 11.2 % / Biso Wilson estimate: 42.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Rrim(I) all: 0.114 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4209 / CC1/2: 0.41 / Rpim(I) all: 0.432 / Rrim(I) all: 1.039 / % possible all: 21.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
STARANISO2.4.9 (25-Oct-2023)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.56 Å / SU ML: 0.3069 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 4216 5.01 %
Rwork0.2112 79931 -
obs0.213 84147 70.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16740 0 337 120 17197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817642
X-RAY DIFFRACTIONf_angle_d0.473124067
X-RAY DIFFRACTIONf_chiral_restr0.03972519
X-RAY DIFFRACTIONf_plane_restr0.00363056
X-RAY DIFFRACTIONf_dihedral_angle_d10.02476341
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.410704516046
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.472073881209
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.572471652257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.355790.271303X-RAY DIFFRACTION7.9
2.33-2.350.3379290.257585X-RAY DIFFRACTION15.68
2.36-2.380.2444470.2413860X-RAY DIFFRACTION23.01
2.38-2.410.3383610.26161093X-RAY DIFFRACTION29.3
2.41-2.450.285810.26811292X-RAY DIFFRACTION34.92
2.45-2.480.3384790.24921419X-RAY DIFFRACTION37.7
2.48-2.510.2952780.2631545X-RAY DIFFRACTION41.45
2.51-2.550.3196950.26781589X-RAY DIFFRACTION42.7
2.55-2.590.3063910.27141757X-RAY DIFFRACTION46.83
2.59-2.630.29011000.28361941X-RAY DIFFRACTION51.8
2.63-2.680.33031040.27632129X-RAY DIFFRACTION56.56
2.68-2.730.31821220.29112311X-RAY DIFFRACTION61.33
2.73-2.780.31431160.29352523X-RAY DIFFRACTION66.52
2.78-2.840.36081420.30152655X-RAY DIFFRACTION71.26
2.84-2.90.33661530.29932892X-RAY DIFFRACTION76.51
2.9-2.970.28381600.27363001X-RAY DIFFRACTION80.82
2.97-3.040.27681730.27263270X-RAY DIFFRACTION86.64
3.04-3.120.28931880.26393402X-RAY DIFFRACTION90.29
3.12-3.220.30671820.25213537X-RAY DIFFRACTION93.54
3.22-3.320.31051960.2553652X-RAY DIFFRACTION97.32
3.32-3.440.29621980.25233758X-RAY DIFFRACTION98.83
3.44-3.580.26661970.23813756X-RAY DIFFRACTION99.45
3.58-3.740.25151990.21193770X-RAY DIFFRACTION99.77
3.74-3.930.23512000.19513779X-RAY DIFFRACTION99.92
3.93-4.180.23561980.1783787X-RAY DIFFRACTION99.9
4.18-4.50.20372010.1633815X-RAY DIFFRACTION99.98
4.5-4.960.19652010.15443807X-RAY DIFFRACTION99.9
4.96-5.670.18992020.17273843X-RAY DIFFRACTION100
5.67-7.140.20712030.18923864X-RAY DIFFRACTION100
7.14-49.560.1982110.17733996X-RAY DIFFRACTION99.81
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)
10.9984108471970.150222417991-0.5543713426540.03323483602160.0009186383631650.978778525306-0.0556374162303-0.245172734256-0.2849387389310.0115203982588-0.0166855371666-0.4085572482760.2415789039090.316893948562-0.1231445905050.5014884689220.0122415712618-0.2022898834360.2496390359680.07415118651030.40877598653736.16881594191.29458101845-34.8486659946
20.0176103982576-0.01072805550440.05398662712090.0150483805218-0.04212837018810.130289654925-0.09291158850770.1263115474680.133823289764-0.336159382598-0.02300069489040.213811156413-0.245305012049-0.228090021937-1.594033542570.686546265570.0841563856379-0.4355920111770.2373603698760.03341886352810.28037412938321.818625539126.786939925-47.9438629401
30.07742685494750.0270408691535-0.2360931283980.0743163364081-0.1448396853540.780021463220.0159543598270.1724749987640.000837186850855-0.0466865332685-0.0181705995550.0222269490060.029152491023-0.11750896574-0.9054915731230.6271565086920.0393673547464-0.3044811767550.2944587857750.008092734505770.3347676450622.771468344225.3280066915-48.4560369784
41.548813983228.22485603417E-5-1.258672270750.1292947487840.0221247602211.12312882963-0.0630586784881-0.070338184807-0.47675610554-0.0664851427997-0.150637898952-0.05395151090560.2913516600570.015326908611-0.3122170965160.5079615211130.0173300052401-0.1725372886250.2554687385580.03209623470210.37586154312439.65373257635.21383468581-32.288905991
50.17014358520.1925054521280.1393145833710.585695213847-0.2306400832880.5483057652210.00178162130551-0.0363333166282-0.0260541948061-0.199776662865-0.02378946595770.138090884419-0.0209988867355-0.06153035036320.01457848277910.4794564596770.0700952362776-0.1866028867980.220492870025-0.01030513034170.28751246034331.195455568423.9327957513-38.7044036208
60.245122231354-0.0713642869831-0.02695587953880.48147013121-0.07474967361630.261474227142-0.02789581406450.06516290902640.0485107359417-0.31907006776-0.0122179038945-0.0877679587083-0.1931058619270.2075065985920.03561820676890.637824039268-0.00848297864354-0.08854452643870.265197632390.05447058525440.2932790237856.63012534443.9768807119-51.8254218625
70.335224611088-0.4257243561060.4906558565010.703591330924-0.363033538951.14385140670.0002337507656390.1692150148840.137455300993-0.417075920649-0.119947577478-0.165700407277-0.1693274579360.2777165003230.02419295263540.786855603163-0.0436794631375-0.07129661678960.2814514014910.02084317882370.29090260585155.976424058442.7777391743-52.8886930752
80.980860189991-0.475194650980.1883455023530.375875317559-0.279896061860.283638048421-0.0583047695154-0.0733735594780.5028517997130.153606119146-0.0697322961505-0.135024804978-0.2117177063440.0542088832247-0.02221780679150.6286670048830.00984832910972-0.1419859132010.202084307868-0.04769113912810.38197066641445.254209199363.6033172228-32.960220327
90.3887208890360.2345988013330.02590790643980.299987834237-0.1974976559340.2925259158770.1236722656070.1008619587910.0441184154383-0.176209674878-0.1509537507370.141697003928-0.164253382997-0.00410204791949-0.01397077359780.5079560289460.0526091857923-0.1418379457290.151658758773-0.002485552169070.24193812981747.960896371745.657356648-38.9823455672
100.008394610507210.02056749679620.001190346888820.05282420526420.00746283103280.112095938739-0.008176972224310.03751295806130.0717014344419-0.1331010522130.0536068670530.00136800323322-0.2468119997450.05472109834860.9275392445270.6093443445220.104823478397-0.3468314176020.01699449470030.1763690527480.02746987626252.487211238144.2186962333-42.7588813977
110.5798942900370.105517032930.9566911821110.08092980579180.339410385762.042631809080.118482361142-0.020195885925-0.151707177940.2148158277780.0437156579643-0.1140098432681.06402857840.09633959476310.3660006339970.4522068728920.0463809308067-0.007889790372760.399911485745-0.04620605683280.33298703656840.524069953623.3807783599-101.559890303
120.327167044024-0.05859298077750.5088880686340.4632895267050.1958608032392.926000034990.1204613030750.0159389629456-0.1353008322670.3944293892750.0196609625195-0.2207218961610.9857327035580.1345901450820.09440771192680.461047758583-0.0144892925242-0.04180081355720.272905828264-0.00491067154180.31792430664539.934956022922.9847153833-103.05378502
130.1244753385760.007905244852380.06002161067210.6533548901780.2451037954480.116497535447-0.08291355855960.195186159790.180670967112-0.001386397052810.190230620787-0.3741422291770.100653972360.3763860717930.4201838957630.2055352947740.0461419896313-0.09741899450850.637954018865-0.1041709465380.44337492493461.83857716338.2786692569-87.5331290977
140.288717802279-0.01925773107540.3676541946860.2744635494710.3543647877820.967896639650.1706839519950.01590753993380.1432422619630.194058611746-0.00833064114938-0.03963866398280.535761844186-0.09664494490462.04307079658-0.0581328487147-0.1713714981120.1273644373370.507395314481-0.02190158468980.22208020857142.102823936932.0755884435-93.5160039836
150.602565576737-0.160386603767-0.150986508960.6468753300740.3519513353630.222676106856-0.288833640901-0.1368939095160.272336390397-0.402943835929-0.2015688199640.0934518943515-0.821752535171-0.650835504677-2.508447029140.5932429950020.262035645888-0.2397993185270.790927534697-0.1872368885780.53132722191626.412627052658.6478128219-108.482853484
160.843800824274-0.1587691393010.4600246476090.07546050030090.1046549128590.968379759574-0.133693158307-0.2117153085760.25222082894-0.0632534397494-0.2887225934590.20728883226-0.524843761458-0.869803805718-1.93329680550.3239882235870.0982344784051-0.08208626381820.743008156061-0.2466665321970.45390052053326.299775058153.8460695699-96.6813516892
170.137257083579-0.1391180756040.05075796800510.157757791704-0.01368210696920.1042866249110.000437755308467-0.0395927111615-0.01024636497-0.0396492724714-0.06940252070830.119082989006-0.0136656193281-0.134747343683-0.3083235939180.3562378629620.358748346964-0.2203744107670.970734040612-0.4155442192520.5609104113365.6357046636354.6891356868-106.455958128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 57 through 86 )AA57 - 861 - 30
22chain 'A' and (resid 87 through 272 )AA87 - 27231 - 216
33chain 'A' and (resid 273 through 308 )AA273 - 308217 - 252
44chain 'A' and (resid 309 through 348 )AA309 - 348253 - 292
55chain 'A' and (resid 349 through 600 )AA349 - 600293 - 544
66chain 'B' and (resid 65 through 272 )BC65 - 2721 - 208
77chain 'B' and (resid 273 through 308 )BC273 - 308209 - 241
88chain 'B' and (resid 309 through 348 )BC309 - 348242 - 281
99chain 'B' and (resid 349 through 426 )BC349 - 426282 - 359
1010chain 'B' and (resid 427 through 599 )BC427 - 599360 - 532
1111chain 'C' and (resid 65 through 272 )CE65 - 2721 - 208
1212chain 'C' and (resid 273 through 308 )CE273 - 308209 - 244
1313chain 'C' and (resid 309 through 348 )CE309 - 348245 - 282
1414chain 'C' and (resid 349 through 597 )CE349 - 597283 - 531
1515chain 'D' and (resid 66 through 272 )DG66 - 2721 - 203
1616chain 'D' and (resid 273 through 548 )DG273 - 548204 - 471
1717chain 'D' and (resid 549 through 597 )DG549 - 597472 - 520

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