[English] 日本語
Yorodumi
- PDB-6wae: Crystal Structure of 6X-His tagged SmcR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wae
TitleCrystal Structure of 6X-His tagged SmcR
ComponentsLuxR family transcriptional regulator
KeywordsTRANSCRIPTION / quorum-sensing / transcription factor / DNA-binding protein
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsNewman, J.D. / Russell, M.M. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124698 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.
Authors: Newman, J.D. / Russell, M.M. / Fan, L. / Wang, Y.X. / Gonzalez-Gutierrez, G. / van Kessel, J.C.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,27411
Polymers103,6694
Non-polymers6047
Water6,341352
1
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8973
Polymers51,8352
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-12 kcal/mol
Surface area19370 Å2
MethodPISA
2
C: LuxR family transcriptional regulator
D: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3778
Polymers51,8352
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-73 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.161, 99.323, 129.528
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

-
Components

#1: Protein
LuxR family transcriptional regulator / SmcR / SmcR-like protein / TetR/AcrR family transcriptional regulator / VvpR


Mass: 25917.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria)
Gene: smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L8G8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M of Lithium Sulfate, 0.1 M Imidazole buffer pH 7.6-8 and 6-10% PEG3350
PH range: 7.6 - 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.13→78.82 Å / Num. obs: 57324 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.055 / Rrim(I) all: 0.147 / Rsym value: 0.137 / Net I/σ(I): 7.1
Reflection shellResolution: 2.13→2.16 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2841 / CC1/2: 0.618 / Rpim(I) all: 0.684 / Rrim(I) all: 1.688 / Rsym value: 1.539 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kz9
Resolution: 2.13→66.92 Å / SU ML: 0.2862 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.905
RfactorNum. reflection% reflection
Rfree0.2553 2946 5.15 %
Rwork0.2106 --
obs0.2129 57220 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.88 Å2
Refinement stepCycle: LAST / Resolution: 2.13→66.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 33 352 6941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656712
X-RAY DIFFRACTIONf_angle_d0.70279101
X-RAY DIFFRACTIONf_chiral_restr0.04331023
X-RAY DIFFRACTIONf_plane_restr0.00451180
X-RAY DIFFRACTIONf_dihedral_angle_d1.81463148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.160.41681430.34332548X-RAY DIFFRACTION99.48
2.16-2.20.3221350.31682545X-RAY DIFFRACTION99.48
2.2-2.240.31931550.28582526X-RAY DIFFRACTION99.59
2.24-2.280.32911340.27262543X-RAY DIFFRACTION99.66
2.28-2.330.2941460.26342550X-RAY DIFFRACTION99.78
2.33-2.380.29311420.25292556X-RAY DIFFRACTION99.78
2.38-2.440.27731280.24022567X-RAY DIFFRACTION99.89
2.44-2.50.29791280.23732552X-RAY DIFFRACTION99.85
2.5-2.560.3211440.23682552X-RAY DIFFRACTION99.89
2.56-2.640.34681280.23962583X-RAY DIFFRACTION99.85
2.64-2.720.26941290.22282577X-RAY DIFFRACTION99.85
2.72-2.820.25731370.21322601X-RAY DIFFRACTION99.74
2.82-2.930.22991440.2192546X-RAY DIFFRACTION99.93
2.93-3.070.26881310.23052588X-RAY DIFFRACTION100
3.07-3.230.28311330.22832603X-RAY DIFFRACTION99.93
3.23-3.430.30711320.21182613X-RAY DIFFRACTION99.85
3.43-3.70.26241410.19092600X-RAY DIFFRACTION99.93
3.7-4.070.221600.18312584X-RAY DIFFRACTION100
4.07-4.660.19951390.15672637X-RAY DIFFRACTION99.93
4.66-5.870.24141580.1832638X-RAY DIFFRACTION100
5.87-66.920.19571590.19062765X-RAY DIFFRACTION99.05
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)
11.49707892267-0.590320364399-2.456960830650.776847546651.753524228315.06306513064-0.2868427331290.2179710371241.589843369260.182552657837-0.259049068434-0.08997806073520.5373571178620.02411720508290.06410751934290.9425880306490.0519148961286-0.2481345500210.74648749099-0.09885925125030.83688555247837.150807212137.209280392-1.99408551854
22.104396920380.3232596782570.6803417928034.074068468240.9950234888070.9668771394730.115208969-1.046430823950.802803040383-0.0279457807063-0.7465356560050.229291975925-0.2307006151120.1144896966870.04201772642070.499617201216-0.164094066549-0.07238508815240.421396004519-0.156250733480.49250424376833.555232546126.8807303487-2.00385656294
31.821334799261.16476939138-0.3853475475923.158069083462.930528263034.51586704334-0.0937479385478-0.00614257173396-0.467877200274-0.147754802385-0.173828806875-0.8975641956410.7053251821340.786162253950.2026658792860.6235495811680.07218823919880.03829938092210.701676224004-0.1483551578771.0661225868742.486042244617.3256151863-7.29839934176
40.954383171638-0.1117899292530.6764525735772.31005294078-1.499647542881.339019520650.545120311325-0.788147593293-0.04595898576260.537172339786-0.820250932265-1.28671486433-0.8982811791260.4406702950420.1210920941150.681770091466-0.157636048949-0.04718323462380.8342728006080.08401411228480.59680420308742.32722441826.61672747921.01843128272
55.387557164321.149324927882.223610287951.404679286570.3757473837442.516563014130.172139054169-0.8570337835060.020092344006-0.0708840767945-0.1663572237660.0198491345009-0.2717242841590.09338007534450.06441293639510.4493671599890.0170500187547-0.05379881724590.435295847682-0.1240074435670.40977260641225.337609085916.925740562-1.37099386511
61.150882897960.3773333298660.2196471241991.73474827573-0.2984930898221.80406492751-0.0589880603958-0.1305905907420.2215649292420.2385619341890.01882949861390.120030358668-0.27997643385-0.03385253402580.05274082222090.3299605537710.0619246963573-0.01220227380.26956881501-0.08132900060480.28822100934919.430417730210.8910801451-8.50826269761
74.340925136560.775495870621-0.4506888112682.1895573718-0.1146022133611.72023150236-0.1089234391550.15282929998-0.193425538780.05421770065730.03088220949520.0789827860270.020171281812-0.2258100590020.04510105976870.3142904035110.0129546929238-0.04421710529190.317854096985-0.03466905176270.31686199711417.23653051484.25368290374-14.2993830931
82.0161202343-0.888996870790.8865630781841.391299733241.072847358942.01157387796-0.1348153269760.1747991856250.433306809862-0.236227848918-0.1013610532480.140744095561-0.104913048013-0.224508988667-0.01194816434920.3236793508850.0827561622497-0.05864815837550.454110892026-0.03643851731450.40321693042211.31321660527.48711461916-23.418674505
92.756864851031.11658375307-1.085731169720.912931537808-0.8338072396294.472093883820.287451110655-0.515636166134-0.1793462309980.817460621811-0.362442708622-0.5929198507030.07121680440250.242472272784-0.06608193563260.560145493747-0.0468217206138-0.01385161259110.7130268516090.1103248184150.61084057875560.2094163841-3.15130288481-11.812140842
106.69849213795-0.835781371579-1.534756980623.01818347464-0.006967095036182.84487922953-0.183682680742-0.483746688165-0.8078767988390.05102617008990.0831951401731-0.03784919152790.2756964986990.3030957595070.1674006855010.290948132353-0.0667236523493-0.04452629348170.5070992710330.02609549254780.35263611822153.1567622288-0.315874803446-18.2376040412
112.21172973791.198750217790.7070096547532.17567812059-0.9371759697721.69614644769-0.0701241436643-0.8267702186610.4760363777640.273816787511-0.131383082472-0.353211276328-0.5311128223530.8806951845670.09560849569460.376925969308-0.0640478669048-0.02846976289370.4659935237010.003547546382160.40205599044557.58331546527.02199971646-17.0986268923
124.789479313683.30556167590.2004858240594.275030604270.4106289216061.3827530428-0.2489503117960.763792673066-0.354518514552-0.1530222462890.354191060812-0.69442968441-0.05210882317310.3365973657270.06575958702840.285527360501-0.01879460641020.03527559383850.7185084186710.03779999868210.35353271430143.63218148970.773227448988-26.7110853145
131.833087579580.253395063883-0.1913172771921.904036080520.3817096221432.49497363410.4034917219180.515673730245-0.974528397049-0.2812247297140.166016508463-0.09616237789870.3197426081180.112469794014-0.0125109347450.3675378652560.00918687089196-0.007093040533190.279826011555-0.04052886647780.36403999523827.4732935185-10.3437006535-24.3098954019
142.69490908309-0.3057242380080.009251991818172.8298515863-1.190486643582.00056189007-0.08965947421710.0568728087120.3250485800540.03668806048030.149814855913-0.180560444306-0.2864266758170.3931979892930.05783399986830.29424091229-0.03609902501630.01682364378840.549264128930.02935954968660.30033173516438.2658372236.03129951271-21.7117434278
157.710441938310.915265497866-0.1733795202371.1830796513-0.9101278265231.13383346857-0.2656712720.7595382955060.194406660397-0.1448802613730.01413889870480.01585283520760.03529204850450.3234684844760.01978066931520.3527297340690.0297490639833-0.00915624152690.6867027477660.008816527876060.27884432969526.1787244635-0.985170107551-34.6529787157
163.092594278870.6515333725721.638958074950.812811848051-0.5787304144553.08099981250.1406286902580.6653288258490.0107108894027-0.146558779734-0.0550982827440.01826986457540.2483669545860.4257117097890.01159823136890.3241991100210.0768163069289-0.009983398095020.375666682723-0.04943510812120.26522652239122.75165167680.661660595549-24.9801465317
171.159211972260.5386944026621.067595073160.9381971145810.3618116280691.558633239790.105472875606-0.152870703627-0.2484685783150.156312980560.0656470807030.07856697397950.0316368325302-0.0197900141587-0.01329070927870.323104890169-0.0457838064471-0.01549190530680.271936205769-0.0622984975760.33071600744623.6697956154-7.85191952457-11.9651908658
181.23283540667-0.787758288123-1.076958345414.870224128446.092089579427.5811809484-0.2418009087050.303999578314-0.339693463893-1.015017105830.1639203752930.7999538858320.6540970007440.0380812166360.09609576938430.641734374483-0.0214432693278-0.1058849828170.470733318253-0.08066333905770.44455743398712.3332756206-8.68501413077-28.9561144966
191.964673579680.5964468081090.08389591319331.50928275885-0.6983626403820.409116060774-0.257365041408-0.08866662375140.123581906395-0.219423187096-0.06025780887490.5732687923220.22819088341-0.7982246443920.0732910839390.471155794368-0.0602058151927-0.02543790445190.353211308866-0.1322531426520.38438435126320.5580584039-15.7243996546-2.34948840284
201.232899029790.6559112331690.6247169934045.509197390042.660140830363.375929201720.07056107814280.066621110759-0.152508014473-0.10502979254-0.2210623455660.206501893956-0.314759674817-0.3465672036690.0548530311620.318359638229-0.07387012411610.007434435913070.310189460274-0.07933812052090.35683184520615.8941134689-24.5605352412-1.48367956758
211.664164776411.156641340970.510915886371.96167101509-0.09035178802871.007492678480.342624953039-0.464345881859-0.2801526883290.1747110771540.0194476874885-0.540232122797-0.1011010736710.216442708968-0.01090270018460.305672682453-0.0654083256717-0.06133343029880.453279407834-0.05283319933460.39554793083522.9957125509-26.63357159952.7946111781
226.941056055421.128777149263.694153404891.646412667390.2662669725053.489717697950.16516006256-0.948838908230.4625410300220.326015111888-0.1898194509530.0582869465317-0.203527650265-0.5259677331950.05103084635810.339927507644-0.0556385827747-0.001756136703460.257693385864-0.1082164890590.2604432679456.54187673064-33.53932551370.0260322584969
233.731478431541.152351971670.5568359011811.850314953540.04867466364061.48957654877-0.0730673985331-0.2744968971640.515332406685-0.144222013532-0.02638301405460.275948801541-0.173053491082-0.0225531376189-0.05694586556950.3368926068490.0372786967549-0.02540094943830.205945860884-0.03468023140560.320334244156-7.10152330035-35.8074153689-14.0743390956
242.864482305630.1951954342970.8871607942743.77785890185-0.6070429701342.79859449197-0.122990316626-0.1771020689290.298944114092-0.5811035249770.273112431544-0.645543160671-0.07618338097650.3644746656610.0451083806910.352230800902-0.06455332942930.02240666944870.279942022495-0.05204331720580.3401995121389.1652690038-33.6491165287-9.11521366453
256.499067154452.289298426120.4554352490932.650636027212.929333670774.2062604937-0.106306871339-0.10084986467-0.1031514225230.3222709798570.099289903206-0.8281092898540.2727713386350.8955444936480.06039991790050.3407019139360.085655478423-0.02798236920870.572698665311-0.008278274715160.51077258117418.0996235145-46.1681303962-4.25090947222
261.838029123890.8225329199360.796079529770.9314411449810.07646821818660.6018787419130.0778522941623-0.0819683941860.2378784821720.211956933483-0.1950244618030.0900046792695-0.05384469414070.07735540814590.01254548011890.338804291199-0.0355673029150.002498921348360.301096954754-0.009628657248340.235104712426-1.33202765022-45.4177906828-2.11311378777
273.645198392541.05393014845-0.7475131236911.81981970926-0.5099530071361.30595112378-0.05245548791670.292016236663-0.186644873937-0.0155496303820.103216051722-0.0222250877377-0.04796929310570.0449127735732-0.0130487651620.269953818117-0.0118865318454-0.007301758408020.228288280201-0.05407932852610.227627603319-1.78092247009-46.5149099698-13.1948589828
282.697860874340.2761853454290.5304242279251.852571225360.9255107304542.390260232490.09548391387950.278068599890.43673264862-0.265606003948-0.1201962241420.337159198629-0.367072764923-0.373784404369-0.1246598012360.3356025506880.0718188427316-0.02663088765480.329359105166-0.03113641141570.329963119963-5.86639040701-42.1955453392-22.6266580183
290.177285951010.31119630372-0.4342674838090.586849142482-0.8159976494091.1071668103-0.2565860705060.00275351340902-0.08715619866660.07672192773210.495658744887-0.3447075985250.2628378075270.4095501503090.06774330607670.6414942427290.1025761133620.1000890897420.887304412752-0.02259360866850.874550535243.9916600729-56.4814656551-13.4640118737
306.60519676979-1.09853818951-2.765922083322.395067375020.6319794774663.39370681596-0.308214270349-0.35588483963-0.6750142649120.3573320086850.13552478035-0.2329318371370.6719497873730.7385348071520.09344540909070.2761877108350.0462948050816-0.04878546433710.799295145839-0.07790887556430.45301973220534.7375120135-51.3366793011-17.6108795144
312.967325261340.5964459630781.064271035480.683587000016-0.06457504360430.925306713777-0.1653983976580.4615061836820.0561508716009-0.02507422085580.446211294174-0.284067700556-0.01776544138220.8079084180760.0573830213920.331052847114-0.01570895650640.07755378593950.824816960768-0.1347063585950.42553062041932.1454706913-46.9670667074-20.7824917557
321.943666579370.448859279339-0.3814818739981.75990701397-0.1949391299212.106318404150.500253308317-0.2621473965-0.793504147183-0.2520403372240.029121166672-0.1300018266820.702775558497-0.25081275042-0.08558080218790.4283769323960.07592740948680.04300791101510.332449663492-0.02189136911370.3630544928268.67655193151-60.8449670402-23.9524806836
332.23160182014-0.4323143087360.09513122324512.72763298807-0.8697279589212.044339665760.0762601119826-0.2921974023540.247632075113-0.1084555909510.00584945967145-0.312221654676-0.1271530832390.873786894690.006239090181620.2922586445-0.09336984264330.03056937265310.604591483328-0.02432216003820.33383000683720.1112297201-44.640496313-20.7808387705
345.39620587370.105450714590.3254700140330.829427405418-0.1264717679311.183699570260.03505813063490.4184384596780.206975544491-0.315620614918-0.004295183167210.04225601071940.164773391809-0.049904447527-0.01085620977750.378581415563-0.00825247124823-0.004703968735850.497844230881-0.04449408380730.270071552373.70878450229-50.9277124559-33.9346276696
352.59219838913-0.3631393738092.335979277581.24474054729-0.1755242672713.35042546822-0.05028830517740.2924661453630.138364153455-0.118962229217-0.259952394368-0.1153161589090.1305040197640.7200081004580.008115580434530.265797053088-0.01354042054550.005330775644650.360010993422-0.03216182603150.2503908821298.67073340783-49.2260070955-19.0173816313
363.74598609366-0.8246306352841.292415597242.5789362904-0.8531956882272.44475541752-0.0523987438787-0.84692566338-0.2943029831240.2009735461760.0741142288614-0.06307285126570.05452079805-0.381999465505-0.01817507628510.3877924451490.005409220135370.01630512753370.308923502548-0.03212892568260.3604624344334.22483100865-59.2126578355-12.2872902358
371.01027594105-0.331251551568-0.6240833729984.142605180884.176198785854.29398878848-0.4925703721940.357816148526-0.528357392703-0.7441504938090.2812561153610.5232230283580.306078544398-0.3372454330280.02728611090.570981728454-0.106081722002-0.0315837140680.44762343679-0.05963626136320.401143961167-6.42683366235-58.3370338839-28.5745735147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 38 )
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 59 )
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 149 )
7X-RAY DIFFRACTION7chain 'A' and (resid 150 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 205 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 13 )
10X-RAY DIFFRACTION10chain 'B' and (resid 14 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 59 )
12X-RAY DIFFRACTION12chain 'B' and (resid 60 through 82 )
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 105 )
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 133 )
15X-RAY DIFFRACTION15chain 'B' and (resid 134 through 149 )
16X-RAY DIFFRACTION16chain 'B' and (resid 150 through 178 )
17X-RAY DIFFRACTION17chain 'B' and (resid 179 through 196 )
18X-RAY DIFFRACTION18chain 'B' and (resid 197 through 203 )
19X-RAY DIFFRACTION19chain 'C' and (resid 3 through 13 )
20X-RAY DIFFRACTION20chain 'C' and (resid 14 through 32 )
21X-RAY DIFFRACTION21chain 'C' and (resid 33 through 59 )
22X-RAY DIFFRACTION22chain 'C' and (resid 60 through 82 )
23X-RAY DIFFRACTION23chain 'C' and (resid 83 through 105 )
24X-RAY DIFFRACTION24chain 'C' and (resid 106 through 118 )
25X-RAY DIFFRACTION25chain 'C' and (resid 119 through 125 )
26X-RAY DIFFRACTION26chain 'C' and (resid 126 through 149 )
27X-RAY DIFFRACTION27chain 'C' and (resid 150 through 178 )
28X-RAY DIFFRACTION28chain 'C' and (resid 179 through 205 )
29X-RAY DIFFRACTION29chain 'D' and (resid 5 through 13 )
30X-RAY DIFFRACTION30chain 'D' and (resid 14 through 32 )
31X-RAY DIFFRACTION31chain 'D' and (resid 33 through 82 )
32X-RAY DIFFRACTION32chain 'D' and (resid 83 through 105 )
33X-RAY DIFFRACTION33chain 'D' and (resid 106 through 133 )
34X-RAY DIFFRACTION34chain 'D' and (resid 134 through 158 )
35X-RAY DIFFRACTION35chain 'D' and (resid 159 through 179 )
36X-RAY DIFFRACTION36chain 'D' and (resid 180 through 196 )
37X-RAY DIFFRACTION37chain 'D' and (resid 197 through 203 )

+
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