[English] 日本語
Yorodumi
- PDB-9t6s: Crystal Structure of the Listeria monocytogenes CadC with Cadmium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t6s
TitleCrystal Structure of the Listeria monocytogenes CadC with Cadmium
ComponentsLmo1102 protein
KeywordsDNA BINDING PROTEIN / Metal-responsive transcriptional repressor
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / : / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLisboa, J. / Morais-Cabral, J.H. / Cabanes, D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)UIDB/04293/2020 Portugal
CitationJournal: To Be Published
Title: Crystal Structure of the Listeria monocytogenes CadC with Cadmium
Authors: Lisboa, J. / Morais-Cabral, J.H. / Cabanes, D.
History
DepositionNov 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lmo1102 protein
B: Lmo1102 protein
C: Lmo1102 protein
D: Lmo1102 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1138
Polymers54,6644
Non-polymers4504
Water3,405189
1
A: Lmo1102 protein
C: Lmo1102 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5574
Polymers27,3322
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lmo1102 protein
D: Lmo1102 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5574
Polymers27,3322
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.004, 64.574, 102.705
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 (eV)
d_1ens_1(chain "A" and (resid 3 through 20 or resid 22...
d_2ens_1(chain "B" and (resid 3 through 20 or resid 22...
d_3ens_1(chain "C" and (resid 3 through 20 or resid 22...
d_4ens_1(chain "D" and (resid 3 through 20 or resid 22...

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_11ASPASPTHRTHRAA3 - 204 - 21
d_12LEULEUGLUGLUAA22 - 2323 - 24
d_13ILEILEGLUGLUAA27 - 5228 - 53
d_14GLUGLUILEILEAA54 - 6055 - 61
d_15ILEILELEULEUAA62 - 7863 - 79
d_16ALAALATYRTYRAA81 - 9582 - 96
d_17LEULEUTHRTHRAA97 - 10498 - 105
d_18ILEILEASPASPAA106 - 108107 - 109
d_21ASPASPTHRTHRBB3 - 204 - 21
d_22LEULEUGLUGLUBB22 - 2323 - 24
d_23ILEILEGLUGLUBB27 - 5228 - 53
d_24GLUGLUILEILEBB54 - 6055 - 61
d_25ILEILELEULEUBB62 - 7863 - 79
d_26ALAALATYRTYRBB81 - 9582 - 96
d_27LEULEUTHRTHRBB97 - 10498 - 105
d_28ILEILEASPASPBB106 - 108107 - 109
d_31ASPASPTHRTHRCC3 - 204 - 21
d_32LEULEUGLUGLUCC22 - 2323 - 24
d_33ILEILEGLUGLUCC27 - 5228 - 53
d_34GLUGLUILEILECC54 - 6055 - 61
d_35ILEILELEULEUCC62 - 7863 - 79
d_36ALAALATYRTYRCC81 - 9582 - 96
d_37LEULEUTHRTHRCC97 - 10498 - 105
d_38ILEILEASPASPCC106 - 108107 - 109
d_41ASPASPTHRTHRDD3 - 204 - 21
d_42LEULEUGLUGLUDD22 - 2323 - 24
d_43ILEILEGLUGLUDD27 - 5228 - 53
d_44GLUGLUILEILEDD54 - 6055 - 61
d_45ILEILELEULEUDD62 - 7863 - 79
d_46ALAALATYRTYRDD81 - 9582 - 96
d_47LEULEUTHRTHRDD97 - 10498 - 105
d_48ILEILEASPASPDD106 - 108107 - 109

NCS oper:
IDCodeMatrixVector
1given(0.999930013871, 0.0117398528973, 0.0014639718024), (-0.0117800788832, 0.999436421009, 0.0314335823864), (-0.0010941211054, -0.0314486281749, 0.999504770716)0.0506834912701, 31.1224982628, 1.92880237761
2given(0.701124071082, -0.113250449981, 0.703988190617), (-0.115322017626, -0.99231823291, -0.0447812113014), (0.703651809633, -0.0497881533512, -0.708798469655)-12.556601309, -74.0217080181, 18.1238763641
3given(0.708050430703, -0.112162204784, 0.697197409203), (-0.0901420653848, -0.993584286783, -0.0682984121798), (0.700384891063, -0.0144880942862, -0.713618314994)-12.5866699719, -42.2132499587, 22.6156447106

-
Components

#1: Protein
Lmo1102 protein


Mass: 13665.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo1102 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y817
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH7.5, 10 % 2-Propanol, 20 % PEG 4K, 15 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2→40.19 Å / Num. obs: 54092 / % possible obs: 98.87 % / Redundancy: 3 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1043 / Rpim(I) all: 0.07059 / Rrim(I) all: 0.1266 / Net I/σ(I): 5.81
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.727 / Mean I/σ(I) obs: 0.64 / Num. unique obs: 5376 / CC1/2: 0.373 / Rpim(I) all: 1.196 / Rrim(I) all: 2.115 / % possible all: 98.17

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.19 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 2669 4.96 %
Rwork0.2043 51114 -
obs0.2063 53783 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.86 Å2
Refinement stepCycle: LAST / Resolution: 2→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 4 189 3666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163527
X-RAY DIFFRACTIONf_angle_d0.41464760
X-RAY DIFFRACTIONf_chiral_restr0.0353621
X-RAY DIFFRACTIONf_plane_restr0.002570
X-RAY DIFFRACTIONf_dihedral_angle_d11.82411344
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.813902262878
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.1463272835
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.919776369993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.36421290.35732563X-RAY DIFFRACTION92.35
2.03-2.070.36521410.3332659X-RAY DIFFRACTION97.83
2.07-2.110.33831210.32012717X-RAY DIFFRACTION98.54
2.11-2.160.34131230.29112772X-RAY DIFFRACTION99.25
2.16-2.210.38941300.28942727X-RAY DIFFRACTION99.27
2.21-2.270.30811590.2742713X-RAY DIFFRACTION99.31
2.27-2.330.3111220.27192769X-RAY DIFFRACTION99.31
2.33-2.40.33351430.25472721X-RAY DIFFRACTION99.31
2.4-2.470.27281530.24632703X-RAY DIFFRACTION98.99
2.47-2.560.27411520.23312718X-RAY DIFFRACTION99
2.56-2.660.23081280.22772680X-RAY DIFFRACTION97.91
2.66-2.790.25231740.22472661X-RAY DIFFRACTION98.03
2.79-2.930.25221380.20672663X-RAY DIFFRACTION96.75
2.93-3.120.2091120.21272752X-RAY DIFFRACTION98.22
3.12-3.360.22081340.19422682X-RAY DIFFRACTION98.15
3.36-3.690.24741510.17272679X-RAY DIFFRACTION97.96
3.69-4.230.2391450.15842666X-RAY DIFFRACTION97.64
4.23-5.330.18551560.15152662X-RAY DIFFRACTION96.74
5.33-40.190.18571580.17062607X-RAY DIFFRACTION96.01
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)
14.374728887351.96592061277-1.64492533334.77657862491-0.3977555079156.19093732363-0.069310874407-0.9091735902130.09373543619360.6540672194320.09805392808-0.09772950234-0.2165854800070.07633010707620.09642234722650.2631611900350.132758370779-0.03081394914920.512660433044-0.06243210089260.399858586039-15.8850630834-40.995130644232.2696664042
25.29255964736-1.66958674674-0.182879007134.60664093431-3.305004738172.76601911238-0.21879537298-0.555087127371.438169778370.9356097150580.484648659709-1.29537239408-2.175501990311.645419425830.3962447369960.797384670687-0.195798593243-0.1439084574260.455846267738-0.16442016760.733041800836-8.64264783023-26.834338997322.9226280697
31.792993222370.811048799993-1.471025326431.5133811449-1.33082165775.76169954420.19615430131-0.006543051817660.1086101769520.06761152202390.003940062194660.0584222624339-0.365398052495-0.148806540891-0.2433473499520.3397671215750.0272939803118-0.003044594263060.311031201244-0.0002027450132280.31261467878-4.9703609177-32.84445060821.1195396049
40.9386510370010.289158296118-1.154105570571.26763414031-1.681878944835.022155666990.109512483530.2068091106470.2484164762680.08753532524540.2284601682180.00928500291977-0.617834702989-0.263689481348-0.2479007506230.3973592632490.02749490624320.02547963644250.3144987784720.01500889840660.309382846775-4.19906695877-27.700030242-8.39982985193
57.18649797685-1.391075944390.4845654251752.175490406551.268345204376.70257951421-0.687549381655-0.147272885712-0.006953781919070.1120853516071.08891888929-0.182019772561-0.5274535442610.406521060464-0.3581351270290.439610749199-0.0208278120452-0.004397387939470.480856128813-0.02162689003570.4009354587811.93779269565-36.63615214897.09270207781
63.615404299612.03019102289-0.9729260764744.02665120637-0.9992902647335.2948630881-0.00919831637763-0.3563754671660.1259588020110.2474198817750.1782775948310.06150591012460.0153272027623-0.0457874102055-0.1688768238010.4180288789680.0926713504512-0.08193077639980.427928158709-0.02326398592620.434342801458-15.6673114201-7.1233722217434.9385556213
72.894073293860.33956673761-1.814519858641.39807940816-1.350591369634.046916889440.04231796923210.0197754080685-0.0581862942967-0.006512442698190.0395447837794-0.07180040004970.1638214297660.251312775836-0.08936843628350.3695332588210.0186920559036-0.01039576783530.312385233887-0.0288074709130.289162844434-5.78587737309-1.200850194565.86267426957
83.043873284042.00370816386-0.1426379680844.84808446064-0.1970849611042.95897845819-0.05776200981490.2268896232750.184040066468-0.2383356995290.2593271179730.5485981741880.389063004965-0.191846885546-0.2849611541870.4221152356860.07270880371950.003649416543610.3140490255680.01387919554470.287068183074-3.52110410901-3.9298675989-10.2959632833
91.09138510348-0.637020894351-0.176875064732.408342500460.4181165021865.220693075650.427076133295-0.06833814218790.03133233218130.1655577994550.138370207992-0.281496091398-0.426278852458-0.543607327786-0.5894475570340.3884133798060.02752249150070.06488840690080.3850274256520.01757006938560.373356142805-7.443555524154.96252050758-3.52886570125
102.63248623155-0.5408852847250.373038471582.57491361342-1.357114743483.60517816377-0.0755871635682-0.296322925088-0.02367360441330.533470231220.116122609034-0.0585257937437-0.4552065251110.189822580191-0.0182048128190.398267606204-0.03270623614370.02442763730390.433936588279-0.06101052879360.3547707370791.038019752810.2706577463933.49943378986
114.07891286275-0.686205572864-0.3270635475022.051641629360.01656143744382.046214642760.4633471013410.3197239601070.227138426232-0.460528646904-0.3133584606620.14462289661-0.470464546833-0.72872774397-0.1123406207760.4252865020920.1039885914740.02897452428470.6163056466210.03098208233750.385312582868-1.25484414296-26.3738101919-17.2992018082
125.307174749862.94314380659-2.227408493459.67347398341-5.796924605433.93559707966-0.121401642660.655392711559-0.975480239857-1.06129390438-0.195323449712-0.7712903718860.7257539621060.4819782589570.4085691835020.3682107418830.0002069908886430.03853773173260.451046679537-0.06396898516630.4454235616097.20767650784-39.1798436796-10.1804208931
132.473438433321.207435465481.491966438168.96064196834-1.69583229621.57581879218-0.4414170832640.370820487046-0.9148122273990.2849417935560.527283403735-0.3369809481011.485133930240.1896478982410.3338943116250.5375710918160.02280331888360.01257680228730.481477621720.04097940689980.5385133327520.663052290667-46.8950289369-2.26060962395
141.982889101910.504307573413-1.398001793521.88551753362-0.6601838229784.03220620430.03327019538090.05872103864450.106836403629-0.250162366653-0.04495571332910.136615687975-0.0455272544761-0.313735442775-0.1012224191950.2797489095570.0259283111191-0.02611203088420.356147908437-0.06059970762430.345017627206-11.928881036-39.325456916912.6371955742
152.730465721781.8987432749-3.760911318765.29509809559-0.533709086786.652248362171.05425594088-0.38479889901-1.834631765320.0261293682427-1.36528451288-0.6384436975790.2551120195840.4154628777250.2591572930770.4844100823350.08150053793810.0002365177853540.4851303217010.05562005591390.500490275596-10.4949646174-45.855573645828.1968465266
163.45681612711-0.403045679627-0.6974633259430.751367336423-0.4702519791842.78462198033-0.1626724238180.0347754806939-0.04776619035360.02674584028860.07119731761630.294597483671-0.19803581682-0.4699156247810.1219974638110.3042066124510.0334893372762-0.01740184869820.3602617996-0.03567398086830.353731407472-21.2140768376-41.43645246521.9790466154
173.941221235372.56299658471-3.379544103526.44601895778-5.285792598124.84469771009-0.0652994784672-0.346137741104-0.515207725335-0.3192644379020.0638796156377-0.07532859682631.703683783340.4453949868470.2689058341270.48349287036-0.01780122635750.01735201205420.4823098307270.00762017645240.495187522272-14.7180381324-51.790109235820.9945067892
184.698677134931.14825293362-3.723790168332.8685072726-2.094924693756.03086816049-0.473791636532-0.0103622436816-0.617336073293-0.2599933817330.1692721284840.03325532994360.7907638826180.121912562990.1102884843980.4233666021830.06517585829150.01225128806960.4219991768110.01076879166740.449024771521-14.6963008283-50.253694329324.6788244263
198.570081274610.3637709876961.082611014297.667777153732.338960422359.44035522916-0.173149491936-1.176701324690.3547636106940.113039138870.2740506033770.250487424762-0.1261967848210.9359022755130.03468078097330.3529548124450.01946260031790.012142042310.558426282425-0.04555305738540.380479649094-1.81542559195-37.781548878116.0436794795
203.25792079606-1.310313244390.1102403158631.66903773523-0.09583230475731.971331880710.189669854417-0.0225877102261-0.01802054397010.101935853195-0.0331849784965-0.161300471038-0.06366696810240.0334655336693-0.05198851370140.4057357913840.03745199941240.04643160418380.574593580428-0.07213135781670.450104307859-1.290479298524.95658725491-14.1970016342
215.735486710912.151405215970.1885726133279.10805782462-0.5080012919363.961421583140.2538763944561.31854615373-1.7162590308-0.408527098138-0.147282546513-1.233566882611.201755831290.920806435938-0.147545936130.6799996541610.1969036312120.02008159656540.665210511887-0.1354623403570.6358136669776.70362704123-8.29876376954-7.38626666613
221.03302004240.377024675974-1.437133455222.505816919873.714181920188.929181777180.2127679519920.471412609794-0.747063066872-0.36978154325-0.407022738853-0.1367962567480.451579266539-0.6157575951330.07508271783790.55631010890.0155881356247-0.009172079792090.359038809949-0.01230204812560.461053702093-8.34794690249-11.80725797296.61398399825
233.856501984771.25615938655-1.112007408613.55834233626-0.7236717729094.12838076284-0.122300539455-0.175322251078-0.0820346803286-0.04170224543120.1130065361440.0202259199193-0.0777064304381-0.05980177166810.04526647465540.2223303642680.00390838553906-0.007137447777860.314301748601-0.03154811105620.285291248672-14.9041988349-7.4044364180327.3255049471
244.35934918555-1.49359714155-2.562006413192.31133322060.5633473195764.39806140654-0.001887753555870.751054068422-0.06056394311680.207308710011-0.171976199252-0.02695498738460.793938986477-0.670784169355-0.06896333975080.32789118727-0.0150994165781-0.03055738425180.4089530845740.009359612193060.322682720403-21.8437746623-12.688476671620.8269363819
252.037846808930.7538898257580.03432507231290.393834050819-0.9433961244577.15699475164-0.188769690321-0.602696561986-0.404031018306-0.2750111102740.0876832172206-0.444533651910.7295948296540.2560331977790.1709516722720.4586784099460.0487705415344-0.006525479021090.2897737987850.01094589464360.458943735826-14.4753480611-18.732816327327.244599619
267.22139975250.1517899286990.9556161270364.426122879441.522074343137.53511598908-0.121280833082-0.635993098336-0.401257334730.3591452449810.152981201099-0.7969972997340.1375505545830.8658831388550.1405594640570.3336682365350.07406720784290.02088536244040.7637122119340.06470757937810.439171996133-2.24066277431-6.8054443654719.1721459718
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 21 )AA3 - 211 - 19
22chain 'A' and (resid 22 through 26 )AA22 - 2620 - 24
33chain 'A' and (resid 27 through 56 )AA27 - 5625 - 54
44chain 'A' and (resid 57 through 99 )AA57 - 9955 - 97
55chain 'A' and (resid 100 through 112 )AA100 - 11298 - 110
66chain 'B' and (resid 3 through 23 )BC3 - 231 - 21
77chain 'B' and (resid 24 through 56 )BC24 - 5622 - 54
88chain 'B' and (resid 57 through 67 )BC57 - 6755 - 65
99chain 'B' and (resid 68 through 89 )BC68 - 8966 - 87
1010chain 'B' and (resid 90 through 112 )BC90 - 11288 - 110
1111chain 'C' and (resid 2 through 11 )CE2 - 111 - 10
1212chain 'C' and (resid 12 through 21 )CE12 - 2111 - 20
1313chain 'C' and (resid 22 through 26 )CE22 - 2621 - 25
1414chain 'C' and (resid 27 through 51 )CE27 - 5126 - 50
1515chain 'C' and (resid 52 through 56 )CE52 - 5651 - 55
1616chain 'C' and (resid 57 through 80 )CE57 - 8056 - 79
1717chain 'C' and (resid 81 through 89 )CE81 - 8980 - 88
1818chain 'C' and (resid 90 through 99 )CE90 - 9989 - 98
1919chain 'C' and (resid 100 through 113 )CE100 - 11399 - 112
2020chain 'D' and (resid 2 through 11 )DG2 - 111 - 10
2121chain 'D' and (resid 12 through 21 )DG12 - 2111 - 20
2222chain 'D' and (resid 22 through 39 )DG22 - 3921 - 38
2323chain 'D' and (resid 40 through 67 )DG40 - 6739 - 66
2424chain 'D' and (resid 68 through 80 )DG68 - 8067 - 79
2525chain 'D' and (resid 81 through 99 )DG81 - 9980 - 98
2626chain 'D' and (resid 100 through 112 )DG100 - 11299 - 111

+
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