[English] 日本語
Yorodumi
- PDB-9t6r: Crystal Structure of the Listeria monocytogenes CadC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t6r
TitleCrystal Structure of the Listeria monocytogenes CadC
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: 3.01 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
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
E: Lmo1102 protein
F: Lmo1102 protein


Theoretical massNumber of molelcules
Total (without water)81,9966
Polymers81,9966
Non-polymers00
Water00
1
A: Lmo1102 protein
C: Lmo1102 protein


Theoretical massNumber of molelcules
Total (without water)27,3322
Polymers27,3322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-37 kcal/mol
Surface area11100 Å2
MethodPISA
2
B: Lmo1102 protein
D: Lmo1102 protein


Theoretical massNumber of molelcules
Total (without water)27,3322
Polymers27,3322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-38 kcal/mol
Surface area10930 Å2
MethodPISA
3
E: Lmo1102 protein
F: Lmo1102 protein


Theoretical massNumber of molelcules
Total (without water)27,3322
Polymers27,3322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-43 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.768, 109.768, 124.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein
Lmo1102 protein


Mass: 13665.920 Da / Num. of mol.: 6
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8% Tacsimate pH 5.0, 20% PEG 3350, 30% 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: 3.01→75.55 Å / Num. obs: 17557 / % possible obs: 99.65 % / Redundancy: 4.8 % / Biso Wilson estimate: 67.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2515 / Rpim(I) all: 0.127 / Rrim(I) all: 0.2825 / Net I/σ(I): 5.12
Reflection shellResolution: 3.01→3.17 Å / Redundancy: 3 % / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 4535 / CC1/2: 0.138 / Rpim(I) all: 0.7896 / Rrim(I) all: 1.441 / % possible all: 98.86

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→75.55 Å / SU ML: 0.5122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3155 928 5.31 %
Rwork0.2598 16564 -
obs0.2627 17492 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7 Å2
Refinement stepCycle: LAST / Resolution: 3.01→75.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 0 0 4966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00125005
X-RAY DIFFRACTIONf_angle_d0.32846736
X-RAY DIFFRACTIONf_chiral_restr0.0325874
X-RAY DIFFRACTIONf_plane_restr0.0014800
X-RAY DIFFRACTIONf_dihedral_angle_d10.19761896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.170.40991050.36762316X-RAY DIFFRACTION98.86
3.17-3.370.34941270.33142330X-RAY DIFFRACTION99.88
3.37-3.630.33691370.30762347X-RAY DIFFRACTION100
3.63-40.30831400.282357X-RAY DIFFRACTION100
4-4.580.24991230.2382378X-RAY DIFFRACTION99.8
4.58-5.760.31261610.24082350X-RAY DIFFRACTION99.68
5.77-75.550.31251350.20132486X-RAY DIFFRACTION99.28
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)
10.02560185705020.02774285255970.006208628111820.02666719236170.008039356440110.002627810086370.1224793922040.008713003049280.2711171039270.304283112958-0.512265048675-0.02999165577520.03528951615130.227350876009-2.08257772172E-50.6160971640810.211754838553-0.1748853988981.517560630440.01882915313651.07599903574-19.5595174999-47.9037242727-18.0109978756
20.00925137022868-0.009968297433820.005570336463790.0317339902430.008278389343930.01076018522-0.0356931151931-0.2008034796620.161539876421-0.06231781120840.1729487598330.00963172366215-0.2344349579240.0410999508189-2.17853254886E-50.749328932133-0.159759727305-0.06748896769130.8248133808750.1106030196690.896459030798-13.9908932358-41.5486655413-13.261615488
30.03006458120380.08825307453280.05251176688830.2932037650470.1909427950110.131264871429-0.0829157075434-0.0233566917713-0.0727751006201-0.0114301314647-0.144910080975-0.1691079439980.06074338581860.221690601594-0.3268012559510.314854661011-0.1659048639450.2823583681280.6686546045020.2535986737230.477551418935-1.2693681778-41.5494331615-9.49138468292
40.3815370891190.04023485584070.2352293437170.02017439239360.07053031583390.272964115356-0.07846801148010.207837247719-0.158194031823-0.1022394714560.00808238533981-0.163716211091-0.08162311256040.235967460023-0.604568831396-0.108443596166-0.18548427765-0.1238257675820.300697258373-0.1191504180970.2878485588531.66419887638-49.1882997644.41184233689
50.828671306470.547629265629-0.4640797416910.903815393788-0.7324575566210.7393523331510.3594289067380.1556819743830.03780285022710.335704986634-0.229666990885-0.0337632577982-0.01510915091330.2576425047280.1612505316360.05108286812580.0400817827583-0.0369531357060.2678112895650.09428462509210.3176980044158.21798665021-44.6738874220.6182387867
60.01823084956190.011457033146-0.02573937094540.00409535362203-0.003296134212260.05343818917550.02370419789350.1417799779070.178229012635-0.136366829503-0.0781526639482-0.0229943226221-0.04000313685090.0850605391542-0.268903470298-0.008962782801560.0967676256438-0.05989238829030.4608562955780.1075306477820.24680720972313.1537380218-50.530625267515.8716877646
70.01820825234490.039915257791-0.02318844252070.0982610875989-0.04028502334810.02202749706260.105302651332-0.009753773211030.339925429759-0.0981252374660.238328520753-0.148044787782-0.161719297981-0.09976124079260.3923641005630.1296071944270.2636993610870.1654214995870.5837843932010.1768968497710.46299473481917.6330529137-43.55815379917.1051735469
80.206837778322-0.2195459189360.2074581191430.311540115082-0.3347194431780.376516493153-0.1140699742230.05498607629580.184193672549-0.0904921287008-0.155380994348-0.357636342629-0.01854395302960.0715093370171-0.5202238237190.5979458255990.08103452791570.01563792340070.0009843831042280.002188320715480.364955272972-0.650439351563-37.357684561211.9942670526
90.003139123097320.00336234017727-0.005372116972920.0070016086289-0.00910400568520.00982377040388-0.2353597840250.0793236241486-0.203588141134-0.342153220492-0.33177537222-0.4496319252290.131026040277-0.420769533554-3.16929009746E-50.818655004018-0.08322965855320.03369804857631.44909655275-0.3331618662431.06598262727-9.77895746621-87.3556520066-2.42671730894
100.101400097801-0.0743526882117-0.02968910632680.0912854139771-0.01444703824740.0352805035407-0.3462785383910.081479684155-0.314526472069-0.156293766793-0.3828284820710.2185983964360.140511511266-0.06626355195860.0002072518122041.011424418690.05706322178910.001789523445570.853112074965-0.05218788446680.544387735975-14.3720371487-71.452115004211.8463338518
110.1560421746130.262916000237-0.1704383081630.616984551357-0.2987217480730.177193382838-0.0132459225918-0.534850113919-0.376572828466-0.00902100002614-0.24072009874-0.09567993729110.0624284247523-0.00169877828909-0.3290970798970.109395394927-0.0304650890147-0.084739616690.471977915072-0.05336506665860.29691663039-17.7511423821-63.475361727930.7422037597
120.308976329882-0.254289141926-0.4408610151310.5666392261970.4304286708030.6472606652260.05398823238390.541176102477-0.08029867011650.027546385461-0.3190314158750.1483625737760.266675235663-0.427402530373-0.04054446447030.5591655906330.186606642696-0.2572588402790.6197472838220.02317461017480.62635456034-25.3068813877-57.996456265726.1544811773
130.2527680574410.05544510278150.01597473759550.02925747559370.04956474577080.127645813709-0.0415142996095-0.2895262029270.1004698937660.0216172655701-0.1536211392580.0741600138230.05524742262070.0571430507914-0.1822955694020.3914316728010.1021313458750.1871425628310.631164041518-0.07345053927630.55936985459-22.7702353128-76.830830803422.5820506402
140.11544327553-0.1694211563710.1950135588620.435479972238-0.4722316852450.5243999992850.176638037147-0.372869116429-0.2101818564860.1006995503220.358894011875-0.10074509975-0.495254704643-0.00785820149510.04137048174240.8053593043470.0472654626464-0.2886609499980.680318795623-0.1819866090440.6830639662948.56859942443-39.90093758529.3647840932
150.243560546630.117052997341-0.02931992112480.182472478952-0.1532318675330.136503164394-0.205335562731-0.320190706456-0.00798264013898-0.00997437486697-0.2542230037030.06300084628960.105358886615-0.0379377776623-0.01073172729660.1938736668480.09496846296610.02711091186620.167690086914-0.03008794707810.16842365184-8.80290431773-47.25912878975.83337407743
160.2796395918440.0237133400449-0.4192885841890.00600830654214-0.03933144832380.62906036784-0.176072216718-0.0486838060415-0.0589267884687-0.26699824049-0.1086016649960.03588114821040.1328727696270.00483922767093-0.4582950444180.4990518530010.1642064795510.1675253475150.183477428227-0.06598412375420.414660529442-12.9966954733-52.7371998648-10.5469057944
170.6564668891720.08356269422490.1836631821410.2016273498770.3469067335380.5983693787570.1618678984890.135745663767-0.00713909880951-0.008907053710660.321234086253-0.09120381133150.0882331427110.203324924441.2290957253-0.1008472815390.03592312710310.001781928045920.189876666446-0.00820104239250.30098565695-16.5533648319-55.1486489070.676962580607
180.3314662511930.4740646383060.163455675441.1697212377-0.1396300083930.3735915676920.1083285934340.214573012001-0.185026276853-0.4313432402340.002315545145340.08552797960920.204354195385-0.04765160123640.8841543702260.283710109105-0.111012114309-0.02919906392780.429549196336-0.381079269270.480002329254-22.2111060928-49.6607327722-1.49002377344
19-0.0003074622605670.0002676089621270.002095391482730.2007715180280.1606841861170.1295752131960.005670204882990.1324691130130.413721087417-0.16826275579-0.275866035159-0.223171204407-0.33178211886-0.101857082832-0.04583059691690.4129218292410.129957317474-0.1077340184350.4237659539910.01580035176290.482933522761-7.62078970658-38.32364290444.12361919568
200.00870772001356-0.00289027520273-0.0002958858157810.001657015895050.001033344084740.02212104491980.180046652118-0.0263515776919-0.04370141740360.05795079703120.1795227823160.0873632446876-0.07216650954050.157805927497-0.0002392632015220.8544577233880.28977521129-0.01418202879421.548825462390.1227043066450.830974372754-25.4292445123-60.856516162443.4330205981
210.02324676399350.0163156362743-0.007872310748470.0192790040648-0.01748494138330.01376035433310.178982581552-0.014049517752-0.279065516690.3051169541330.08942070051320.0662825480979-0.2468440944760.0971694447742-0.0001110019062320.527587984958-0.1701162038450.04482805704920.5872213793130.04359711525520.705692961137-25.3778053737-69.399631812440.4228282278
220.3851240517120.659416697267-0.4273690151942.33816987791-0.1580913157060.745787723322-0.3896978141150.0705092892207-0.161167097087-0.0856380214541-0.485309274543-0.3740156141840.154509015887-0.0448576186638-0.03250850080241.40534776215-0.1584774743540.001575308938090.6338836191770.02760735722840.338747126727-16.7968900646-78.38570260436.1149632722
230.2169295755750.5326867469830.2895825308351.752654367910.216867149910.956089705644-0.3955383388170.212607745932-0.2858126412370.622481648284-0.1055429277520.6116790784460.332147200828-0.234790754916-0.7939983385880.3886587544030.193452450260.1240461125420.759969171796-0.1011694409730.529672066249-8.81111213413-77.536182684215.6460175132
241.499642190040.3681727198241.457784934430.1129080712530.3467771056831.42106773076-0.1831168439020.986978372935-0.139754320308-0.324058471428-0.465030643330.2743705965370.1689415583040.147538966431-0.2332227032090.70920579880.2260943461430.3264288565680.7572572428110.1080296906890.750027437905-3.70189541395-84.11507272942.44314105118
250.0739751652461-0.09626935906350.1892840033580.163800361677-0.2775310878790.4982011022680.130726258261-0.3720500507860.2497506220020.30455176933-0.3174633002840.295043446059-0.4571882151020.321332708736-0.04983394595110.5978532270380.2092778074050.1882954742910.466562132550.1195073661560.4981420912210.858667722523-81.370254323212.5943706971
260.1793911868880.1330650736680.1898695400010.09866081925950.1414556704190.2025646562530.08702018277240.171265813976-0.03729539581630.00610341140863-0.0420183194647-0.0187485471368-0.01006727232530.0290217556962-0.02956750944330.9496223349260.4184576398430.4665120661160.877711561936-0.1291029479591.311606411735.84440979822-93.85647071724.81232942411
270.0170544892974-0.008064348302450.008738111180050.0363624458192-0.02835566473190.0210361041359-0.112669501108-0.3758144443690.183225135542-0.264630529868-0.172266742406-0.003764479220910.244499662392-0.3965325628880.0001053210086270.9498903428310.2730887156930.2048785347680.700889453540.0326045813221.13609978668-3.79843149604-88.8482470912.6449245192
280.1725880570460.1499796492270.09995082030840.2328863435720.03994154935720.0774870395152-0.296927551094-0.0118127158992-0.00144985920316-0.1164015932730.03823139595890.2415600155660.0355238169898-0.05603124840050.06816841138011.17062001268-0.04379722692740.04317608980461.02528507099-0.3761354634750.568424151128-17.8332718637-83.083850663315.1454195633
290.0468274520061-0.05488138441180.005564976998890.0539903379467-0.002038292745480.00224802617689-0.4099318745190.1533328906420.230295551904-0.1895454961490.298514744414-0.583084979573-0.07437714828810.33968533597-0.0001005507394430.59932159889-0.04733693176290.07769258346750.77172606999-0.1010112333530.8467034540468.15498257074-22.5092021561-4.02070139757
300.2316071042990.05720445039660.03341423422220.0732779979001-0.09377209722790.175185331465-0.291715686174-0.3077408851590.0281216267982-0.2098319998360.00593586232251-0.11671535828-0.0840473044617-0.0147569742855-0.3500080275520.9099109355160.41628426240.1712105409460.7753125728730.1294102403720.424483029815-4.23954629766-14.24586070213.3463755839
310.603656503457-0.7682296403830.2862166653260.988463667768-0.478355113660.478384189712-0.1757665329520.1893700861750.1217337946690.0983099336856-0.030328568916-0.5442928285050.07261009489730.0708963963581-0.1422164729760.4372144190090.2760414187330.05666639773080.436053373393-0.3401859424350.447200593292-11.720198469-13.925593049828.4306979041
320.1876702489590.0325115647621-0.09660140290040.6675346202-0.5114689831410.3818644304470.675570992563-0.337428380275-0.061389812104-0.0656208308476-0.790530108021-0.0426667398766-0.062328545308-0.214861711765-0.1201742990640.7997881393470.02489019717180.04677648245160.707181975998-0.2252565410410.557079875925-13.6554118081-20.982118623522.7772366088
330.01239352911410.0209430881441-0.009907786634440.0326922893652-0.01362510107730.01164239911670.236303040289-0.2682497416350.0912723407457-0.002399437401310.1825660892360.3683388430650.389843478427-0.06497383835570.0001110730560651.079184819530.4140655252810.1042784351711.084720575670.06005928888341.235064404-13.2137835319-22.46990249738.4752317874
340.004835719420710.00173107632593-0.0026354917372-0.000318012341776-0.0008581608345250.000427717455698-0.0763046736607-0.09053645759410.03098955026980.0734612893781-0.105394531051-0.121945561725-0.1848998688110.1055295293232.35695349233E-51.040765496610.3701108067010.01042038341860.5581041214450.0438200665460.6206548893270.280798131368-22.313010256633.88295276
350.0946543762409-0.0456429894075-0.04352046196430.06546150187560.09064578252160.1280438667340.248349335795-0.384622134793-0.319943953197-0.328447803278-0.567829192997-0.140285599902-0.234462235624-0.0525723160623-0.008722288636520.554893313071-0.03848774964170.06137110355450.309132286770.0786831458690.6220831304144.67367542141-16.127594131413.1549927256
361.02271279798-0.682387912006-0.5103512449040.4535461527830.3440021992410.258045944098-0.03961837673270.57134300543-0.44818608542-0.4354904886070.0427268555342-0.503969181224-0.284743658034-0.162498942129-0.1103621138380.486006516982-0.0772887531857-0.1293837848970.4071107395450.1929553603560.53396380978413.3810562643-15.99388188170.188541111102
370.0794942627436-0.1969081841780.06626022761540.639646102956-0.4179307710990.4001823593760.05473458266060.01830594782590.1182813825110.628897447341-0.190654333829-0.404456468812-0.0269487897072-0.06893218489160.2345176376930.575126518278-0.0405951866784-0.08756985970310.6997493592310.2833574851930.43030134462315.3470970944-11.39276152239.85667178634
380.1947101168850.07845690516220.04125976331550.02498105296570.02050643987980.1544172903970.3733039477780.0113165973215-0.152398166268-0.5881868913490.1785221144620.0609588970778-0.1776503770620.210792232530.03428592621850.425985122212-0.10766513649-0.01396943083320.1654656452020.02376481769880.46371385255620.0405430765-17.42678856867.50901100324
390.007624066770720.0199193343704-0.01711195294270.0346149939362-0.03473441818320.03114495618280.0734423547853-0.0228431945105-0.4049961363930.0159531654406-0.2243762671570.08555274148190.0975413987698-0.118322028006-0.0001885567480330.5797845753880.1257968238810.02195780417590.570382772068-0.1120105421180.638753930423-0.524215040328-26.592566384411.2624601037
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 11 )AA6 - 111 - 6
22chain 'A' and (resid 12 through 21 )AA12 - 217 - 16
33chain 'A' and (resid 22 through 26 )AA22 - 2617 - 21
44chain 'A' and (resid 27 through 39 )AA27 - 3922 - 34
55chain 'A' and (resid 40 through 64 )AA40 - 6435 - 59
66chain 'A' and (resid 65 through 89 )AA65 - 8960 - 84
77chain 'A' and (resid 90 through 99 )AA90 - 9985 - 94
88chain 'A' and (resid 100 through 112 )AA100 - 11295 - 107
99chain 'B' and (resid 9 through 21 )BB9 - 211 - 13
1010chain 'B' and (resid 22 through 39 )BB22 - 3914 - 31
1111chain 'B' and (resid 40 through 80 )BB40 - 8032 - 72
1212chain 'B' and (resid 81 through 99 )BB81 - 9973 - 91
1313chain 'B' and (resid 100 through 111 )BB100 - 11192 - 103
1414chain 'C' and (resid 8 through 21 )CC8 - 211 - 14
1515chain 'C' and (resid 22 through 56 )CC22 - 5615 - 49
1616chain 'C' and (resid 57 through 67 )CC57 - 6750 - 60
1717chain 'C' and (resid 68 through 89 )CC68 - 8961 - 82
1818chain 'C' and (resid 90 through 99 )CC90 - 9983 - 92
1919chain 'C' and (resid 100 through 111 )CC100 - 11193 - 104
2020chain 'D' and (resid 7 through 11 )DD7 - 111 - 5
2121chain 'D' and (resid 12 through 20 )DD12 - 206 - 14
2222chain 'D' and (resid 21 through 26 )DD21 - 2615 - 20
2323chain 'D' and (resid 27 through 51 )DD27 - 5121 - 45
2424chain 'D' and (resid 52 through 67 )DD52 - 6746 - 61
2525chain 'D' and (resid 68 through 87 )DD68 - 8762 - 81
2626chain 'D' and (resid 88 through 93 )DD88 - 9382 - 87
2727chain 'D' and (resid 94 through 99 )DD94 - 9988 - 93
2828chain 'D' and (resid 100 through 111 )DD100 - 11194 - 105
2929chain 'E' and (resid 9 through 26 )EE9 - 261 - 18
3030chain 'E' and (resid 27 through 39 )EE27 - 3919 - 31
3131chain 'E' and (resid 40 through 80 )EE40 - 8032 - 72
3232chain 'E' and (resid 81 through 113 )EE81 - 11373 - 105
3333chain 'F' and (resid 9 through 20 )FF9 - 201 - 12
3434chain 'F' and (resid 21 through 26 )FF21 - 2613 - 18
3535chain 'F' and (resid 27 through 51 )FF27 - 5119 - 43
3636chain 'F' and (resid 52 through 67 )FF52 - 6744 - 59
3737chain 'F' and (resid 68 through 89 )FF68 - 8960 - 81
3838chain 'F' and (resid 90 through 99 )FF90 - 9982 - 91
3939chain 'F' and (resid 100 through 116 )FF100 - 11692 - 108

+
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