[English] 日本語
Yorodumi
- PDB-6v6n: The crystal structure of a class D beta-lactamase from Agrobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v6n
TitleThe crystal structure of a class D beta-lactamase from Agrobacterium tumefaciens
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class D beta-lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsTan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of a class D beta-lactamase from Agrobacterium tumefaciens
Authors: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,70310
Polymers111,1924
Non-polymers5106
Water7,044391
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9363
Polymers27,7981
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8902
Polymers27,7981
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9863
Polymers27,7981
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8902
Polymers27,7981
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.119, 101.655, 108.142
Angle α, β, γ (deg.)90.000, 97.841, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Beta-lactamase /


Mass: 27798.094 Da / Num. of mol.: 4 / Mutation: D195Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: oxa, AtA6_05530, BV900_07365 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A1V2APZ1, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15 M DL-Malic acid, 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 25, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→46 Å / Num. obs: 102685 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 27.72 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.075 / Rrim(I) all: 0.133 / Χ2: 1.895 / Net I/σ(I): 15.92
Reflection shellResolution: 1.85→1.87 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 3294 / CC1/2: 0.642 / Rpim(I) all: 0.369 / Rrim(I) all: 0.632 / Χ2: 0.365 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→45.92 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.0628
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 5113 4.98 %random
Rwork0.2114 ---
obs0.2132 102587 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7634 0 32 391 8057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00447985
X-RAY DIFFRACTIONf_angle_d0.710810882
X-RAY DIFFRACTIONf_chiral_restr0.0481163
X-RAY DIFFRACTIONf_plane_restr0.00551435
X-RAY DIFFRACTIONf_dihedral_angle_d17.13554749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.32651600.28382835X-RAY DIFFRACTION84.72
1.87-1.890.36091560.2763257X-RAY DIFFRACTION97.63
1.89-1.920.30991670.25633311X-RAY DIFFRACTION98.81
1.92-1.940.28081800.25693301X-RAY DIFFRACTION98.7
1.94-1.970.2981720.25013258X-RAY DIFFRACTION98.71
1.97-1.990.29131680.25323349X-RAY DIFFRACTION98.57
1.99-2.020.29381700.24293239X-RAY DIFFRACTION98.38
2.02-2.050.33951580.23863312X-RAY DIFFRACTION98.16
2.05-2.090.27311840.23223291X-RAY DIFFRACTION98.22
2.09-2.120.28111670.2323214X-RAY DIFFRACTION97.46
2.12-2.160.29821650.22483270X-RAY DIFFRACTION96.98
2.16-2.20.26841700.22453180X-RAY DIFFRACTION95.91
2.2-2.240.28521790.22043314X-RAY DIFFRACTION98.2
2.24-2.280.28551710.22333262X-RAY DIFFRACTION98.82
2.28-2.330.2691930.21883308X-RAY DIFFRACTION98.81
2.33-2.390.28081890.22363262X-RAY DIFFRACTION97.98
2.39-2.450.24291590.21983284X-RAY DIFFRACTION98.12
2.45-2.510.27791840.23163277X-RAY DIFFRACTION97.77
2.51-2.590.28781750.22663223X-RAY DIFFRACTION97.06
2.59-2.670.28481590.23143242X-RAY DIFFRACTION95.99
2.67-2.770.2751720.22993307X-RAY DIFFRACTION98.39
2.77-2.880.26841630.22733275X-RAY DIFFRACTION98.12
2.88-3.010.23841610.223294X-RAY DIFFRACTION97.57
3.01-3.170.26231620.21983279X-RAY DIFFRACTION97.01
3.17-3.360.24581740.22343216X-RAY DIFFRACTION95.95
3.36-3.620.22881570.20123242X-RAY DIFFRACTION95.83
3.62-3.990.2311940.18913233X-RAY DIFFRACTION97.14
3.99-4.560.20981650.17073231X-RAY DIFFRACTION95.61
4.56-5.750.18781570.17473197X-RAY DIFFRACTION93.84
5.75-45.90.20341820.1983211X-RAY DIFFRACTION93.57
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)
15.36839473512-5.772978302410.3783451914726.32862421863-0.6317781227361.595985718310.02260308049550.06662514563350.29215533973-0.0749329759950.1209754113340.0868193640031-0.637099274417-0.208351640688-0.1908947869670.53443150890.0767708911054-0.0823141832280.3576343426650.02874296485220.513437647366-12.9710966181-45.647855748417.9223201265
23.066351345660.3687693457231.07672295822.59491542758-0.03397624251072.08247080680.2246011466580.343006318492-0.115592262323-0.2851282135460.0802221477187-0.1039773098610.001467841854540.160577222177-0.2787505222860.2969530403440.0213209599458-0.03474814556220.293610134284-0.0674896228590.2716446446212.20476953324-52.794977118619.344929689
31.55641177083-1.37310368481-1.386959347394.305548106480.8336634496191.38991325675-0.9297432871660.004802599694680.498280552720.662178157386-0.04170008147110.0861692612662-0.321851449270.3165673574990.4039354313780.347052394572-0.225296512486-0.2796998285050.588714725697-0.4340096956970.84847796827817.1735041663-41.958211092734.1511465421
42.38303740586-0.3843601132730.1083917895842.97658103681-0.7632222558033.722820225340.0727220266442-0.03675371969530.678969100031-0.08058809846160.152095175841-0.801072778293-0.455956224070.505074006583-0.1877645611490.260457622734-0.08798399209190.07347586671310.348865952207-0.08495338851490.55217486002812.4448800431-41.465429095524.0133443729
52.219826447020.800665862559-0.9034894371452.48835188235-0.3488536037352.43910536253-0.0993740221999-0.006785717714240.0891451943993-0.0895283824470.0984133878882-0.3056545273720.07752362649330.1683991069390.01799540276780.18941333348-0.008729510237310.01248099846820.27165415601-0.04786978538510.2357705664495.89972332351-53.756536688923.0857952718
63.60144884866-3.329902288820.7256688329713.19862312278-1.581248302993.240179040520.1078658986510.03549407480830.3314928626680.0282874004925-0.1762636992320.000891972132679-0.302198586235-0.05327921791190.08632841946410.2003551868610.0165998017351-0.03538284835540.27166277214-0.02379427962340.262669484342-5.52075689197-46.95890448324.5305135695
75.327860924251.38097266442-0.102116172754.472218215194.503162983576.285955188110.0639937492814-0.2545893391670.306855784628-0.34149487861-0.8005992672661.861514919270.124594885914-1.032338261990.5473162372430.2575521105550.0183755158401-0.1100171832560.3409315235590.005475315422410.328860645767-9.20951844973-56.973958162629.570757238
86.32318464385-0.603491749826-1.11195514016.03972627007-2.29884214454.15787774479-0.0871985953564-0.1849886903150.108582428231-0.4737956201210.1449956568910.613826640884-0.0963746294579-0.246632471467-0.02226889250690.2356517186850.052144834516-0.1030618617250.313933276628-0.06854341891390.26909604893516.2525383296-14.1946269743-11.3756504859
94.05332455784-0.08945348134970.5427337577922.03805354633-0.1536442527873.07119498260.06529249161380.15009813944-0.253689472389-0.188431741886-0.0981696732973-0.1752442931990.5898182968120.3829790853650.04825246455390.3504338895250.195843483435-0.02004573812040.34662800025-0.03156917444310.24564420801332.4513610115-25.84356922124.81995692487
101.37306917670.1286729631390.08235548515440.8190891621020.1497795772342.32078282554-0.05701047171780.0134109909197-0.05916300426940.01518267773550.0676718690162-0.1883903160430.1593835233950.1294629495420.02257689740260.1491213117990.07832150450410.002739436396080.243150123821-0.02795095612650.23196268055626.590878382-15.125025728-1.44582505986
113.47077912918-0.1057653318310.6058276270042.329820670441.120527903133.298795071370.08984263329550.303103082455-0.135944909163-0.318708461326-0.21944232282-0.1235850150550.3089841165590.01746947777220.09928890735220.2168193681160.03391779088550.004593792132910.328163629334-0.05179727982560.23230475326425.0456785937-18.4459970062-13.8959405897
123.7354345344-1.975133539750.3126905306335.30653641637-1.971497293771.991470787360.1808443010230.01751492677040.147978455419-0.385322068025-0.3022186998460.3078731404730.0825729159276-0.2481182332810.1658088348720.2311753187230.0573024509551-0.1078010332110.276248774126-0.05028543593770.319170787269-22.9330288916-15.619056482243.2104933985
131.375762962490.2560536978820.8710626371.453533689341.73979845358.046193183680.0718153136823-0.1371473337880.127663158960.08284247500170.100583844242-0.13447742353-0.1123581243050.367842764879-0.2281434500590.110023189735-0.0312237264963-0.01419549119340.1557840164650.0008869429425960.200645719552-8.86645676924-21.241812303758.3591254916
142.07426097746-2.05943416648-0.3106054158917.722478805232.747018488915.978817727150.055047411014-0.172465064957-0.4949289621620.05838461746910.0342347132431-0.6925603387150.5845224387450.496770968011-0.09784092134770.2367525534110.0359852109721-0.05527091925020.3639457492170.09952569854490.4914485089152.75563764327-28.37348266558.2894663205
155.49554928895-1.31646608712-1.576934117764.14447074820.5772490584634.158920466310.105116054661-0.118045310816-0.1144343901420.0291754772898-0.212805771878-0.3418686236380.3276660456130.3840098484940.07614120537710.12528690801-0.0115860861089-0.05899510670290.2023723014720.03428927696690.245473554594-4.91995180367-27.015963452758.5282098755
164.429566380790.0420707740598-0.08145966443312.10630764581-0.4359424573533.61086117572-0.0946466131457-0.057987953459-0.2342956780390.199328966628-0.05251161019520.1609702593660.510193983562-0.3230210040460.1322505519460.221499122772-0.0774760660995-0.007181572159840.186786267506-0.01449463314780.248184855664-18.1206922628-31.532706298857.4254165894
173.6903891884.189381462645.276861998965.196302780837.018114580189.672324250380.00817147527686-0.113864101514-0.178531234943-0.37035448994-0.116559530104-0.262267577084-0.257782405405-0.3569156233550.1929092681530.1425340011650.00314967076728-0.01418773203590.164541742085-0.004939395302940.195239116369-17.7525773829-12.728457219553.4056059134
184.19303854025-0.687572165828-5.721975736974.710103219781.266363173098.054350985460.3622307782960.06215764589560.4778151101540.0813887832761-0.122106147095-0.508098250773-0.622920136356-0.0534147891584-0.2221009689160.19275412465-0.0125565718634-0.002057056936180.2880872984660.02775668340140.21717876256-8.38035115461-11.074783366761.1037759839
191.855561168120.547676549341-0.5893544129125.56788242203-2.122471733053.626929164180.5269730496220.5495634662870.3535056570160.339620834389-0.301904184653-0.0990310811081-0.235466321910.364324712076-0.1470660097140.1288714367150.03928865484240.1186846388040.2860787183860.09978615212270.339156761456-6.33458286395-12.851886357242.4558819862
203.19329905369-1.7700752557-0.2819955731634.674403702460.4633884059924.157002100380.55888752114-0.11021069756-0.4003897807710.195831572704-0.8485385464460.6204892774091.00389566762-0.4683505559420.06894437591860.318081913074-0.0419678180631-0.03641417202230.276494862357-0.04942490997170.322773651276-16.8371781888-28.052077995744.2398562169
214.036573831110.760212631182-0.27872379762.073337234882.442437767213.39470658560.07152657536390.368936601382-0.0988833159935-0.8563418032560.1054788034-0.246715964154-0.1292952410360.151197996283-0.2564197645820.299740580670.05294177315610.03422394778650.302892773012-0.003102759297790.228165912151-14.8083470312-18.780263210139.7566504814
227.803020964642.951892509630.6747078203788.26074616659-0.3144527877312.360000397740.2297727807350.9634840151490.748214443213-0.471669581927-0.426939742994-0.713378915454-0.5528653043070.01229363271530.08287339150210.3385904258940.06778511874360.07088428630270.3686936304450.03815031658630.306440182222-12.2918138453-14.000976675636.2432776443
233.22176292256-0.9481888850460.777693293033.4941902606-0.0009885531076562.41602815136-0.0791568146823-0.2530439276880.1760928813730.3554992295910.0679263772046-0.4760150363540.05250944115220.1312972651180.0003182448814450.2034036079490.00833027563021-0.02682931378560.1691394866340.01147818892530.2210856441820.0877078378-2.8867192942734.7681994505
242.16971939006-0.104804596256-0.05066569081665.07102880010.4036266714033.21773282987-0.01566407701480.3505693792590.292375317159-0.806864892745-0.0003157077952260.0899197951373-0.42716683546-0.108494927926-0.04799974885770.3357381064850.0663649973909-0.03912021392330.3099848211730.08175485864760.2459722223065.575050475696.4298142957218.4011101063
252.760603389730.5833295158860.117523859071.751936004470.6260478538643.842585690370.101234964781-0.1157188064810.3868754081150.0122519931308-0.09114451734070.271127345186-0.281418428988-0.231907616550.0286732076670.205922932990.05334039729550.02525553535060.17818676889-0.01723851997290.2306622949676.814195129028.675868652235.2898619274
264.686238975244.911069157793.649014138665.11780432733.827155548342.877893880610.247878577672-0.492086820393-0.02775710004820.919844560608-0.2730091896450.03335832494970.455395139363-0.0378899815662-0.01306383111530.2993981438070.05400353736350.0359174558120.2624387675320.02064381531220.25771758301214.7376130909-7.9868213721236.6572774027
275.54599438962-0.407259212333-3.744263515324.47055368277-0.3698467304867.56537336596-0.2233354771550.0884426564591-0.293662226568-0.07311484580950.00992199056060.191544268180.804611218056-0.244360218240.1955188523270.1502723479670.01057073353260.01766595407030.157036162378-0.009036659161520.2269732467455.36761528893-9.3203782375429.9674276442
284.07187940725-0.0103585897412-0.7151498673875.072680221841.535759995764.35848604030.125479279655-0.02685274116030.5415320524170.250923879397-0.233701242698-0.0637226569755-0.2376516859310.225041863830.1121066489730.1929494962640.00762734515277-0.02260617519080.1776003528830.02577496164970.17763200742822.4056373781.0456379549427.6006526274
293.423387839770.795787761245-0.6453412929375.146067347640.265106629714.21142183539-0.2676702562950.3873279571250.101415114004-0.2316044959170.438871117695-0.591114211363-0.1374231586240.489866489511-0.1490432452140.155053779706-0.0186494507132-0.02495183065450.302001057197-0.01075672376480.2316394406626.6358886684-1.0172102009527.974950364
305.672614040971.24213860872-0.8834500644314.99980541823-1.318252357347.21630046862-0.110873832605-0.05042712917490.172624198533-0.259624222565-0.246376410007-0.9469573859340.2932114371780.7007916271230.3117486747980.2340153648760.01650976831590.01154361049410.229934264174-0.0130446193910.26038687653728.752860016-5.4046813263223.7205623863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 147 )
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 209 )
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 253 )
7X-RAY DIFFRACTION7chain 'A' and (resid 254 through 272 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 147 )
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 273 )
12X-RAY DIFFRACTION12chain 'C' and (resid 28 through 57 )
13X-RAY DIFFRACTION13chain 'C' and (resid 58 through 72 )
14X-RAY DIFFRACTION14chain 'C' and (resid 73 through 92 )
15X-RAY DIFFRACTION15chain 'C' and (resid 93 through 132 )
16X-RAY DIFFRACTION16chain 'C' and (resid 133 through 161 )
17X-RAY DIFFRACTION17chain 'C' and (resid 162 through 174 )
18X-RAY DIFFRACTION18chain 'C' and (resid 175 through 190 )
19X-RAY DIFFRACTION19chain 'C' and (resid 191 through 209 )
20X-RAY DIFFRACTION20chain 'C' and (resid 210 through 233 )
21X-RAY DIFFRACTION21chain 'C' and (resid 234 through 253 )
22X-RAY DIFFRACTION22chain 'C' and (resid 254 through 273 )
23X-RAY DIFFRACTION23chain 'D' and (resid 28 through 72 )
24X-RAY DIFFRACTION24chain 'D' and (resid 73 through 109 )
25X-RAY DIFFRACTION25chain 'D' and (resid 110 through 161 )
26X-RAY DIFFRACTION26chain 'D' and (resid 162 through 174 )
27X-RAY DIFFRACTION27chain 'D' and (resid 175 through 192 )
28X-RAY DIFFRACTION28chain 'D' and (resid 193 through 233 )
29X-RAY DIFFRACTION29chain 'D' and (resid 234 through 253 )
30X-RAY DIFFRACTION30chain 'D' and (resid 254 through 271 )

+
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