[English] 日本語
Yorodumi
- PDB-6kw1: The structure of the metallo-beta-lactamase VIM-2 in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kw1
TitleThe structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Antibiotic resistant / Metallo-beta-lactamase VIM-2 inhibitor / Trizolylthioacetamides / Crystallographic study
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-9RX / ACETATE ION / FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77521201035 Å
AuthorsYang, K.W. / Xiang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81361138018 China
National Natural Science Foundation of China21572179 China
CitationJournal: Biomolecules / Year: 2020
Title: Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-beta-Lactamase 2 (VIM-2) Inhibitor.
Authors: Xiang, Y. / Zhang, Y.J. / Ge, Y. / Zhou, Y. / Chen, C. / Wahlgren, W.Y. / Tan, X. / Chen, X. / Yang, K.W.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24922
Polymers56,7062
Non-polymers1,54320
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-111 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.759, 79.421, 67.981
Angle α, β, γ (deg.)90.000, 130.938, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase class B VIM-2 / Beta-lactamase / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 ...Beta-lactamase / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta-lactamase VIM-2 / Subclass B1 metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 28352.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2, IPC669_36195
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0

-
Non-polymers , 8 types, 344 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-9RX / 2-[3-[2-(1H-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1H-1,2,4-triazol-5-yl]benzoic acid


Mass: 394.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N6O3S
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.1M MES, pH 6.5, 0.1M magnesium acetate

-
Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.775→39.1907632483 Å / Num. obs: 39958 / % possible obs: 99.13 % / Redundancy: 10 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Net I/σ(I): 6.38
Reflection shellResolution: 1.775→1.839 Å / Num. unique obs: 39958 / Rrim(I) all: 0.14 / % possible all: 99.13

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ko3

1ko3


Resolution: 1.77521201035→39.1907632483 Å / SU ML: 0.164202998798 / Cross valid method: FREE R-VALUE / σ(F): 1.38229043876 / Phase error: 21.0323134189
RfactorNum. reflection% reflection
Rfree0.206324845679 2019 5.05407029138 %
Rwork0.176544854667 --
obs0.178080634821 39948 99.1388509741 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.9373964541 Å2
Refinement stepCycle: LAST / Resolution: 1.77521201035→39.1907632483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 84 324 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392522518413640
X-RAY DIFFRACTIONf_angle_d0.6856642335734976
X-RAY DIFFRACTIONf_chiral_restr0.0495713551409560
X-RAY DIFFRACTIONf_plane_restr0.00398587243297654
X-RAY DIFFRACTIONf_dihedral_angle_d13.31346546222098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77521201035-1.81960.2221154888541300.1919431486352457X-RAY DIFFRACTION90.1707912165
1.8196-1.86880.2345370891511490.1865329677772747X-RAY DIFFRACTION99.9654815326
1.8688-1.92380.2420431139271450.1797716661452706X-RAY DIFFRACTION100
1.9238-1.98590.2191308852411380.1827213741612715X-RAY DIFFRACTION99.8599929996
1.9859-2.05690.2251877035871430.1709630555052687X-RAY DIFFRACTION99.4378074491
2.0569-2.13920.1809313933521430.1735654343342724X-RAY DIFFRACTION100
2.1392-2.23660.1931587875571460.1733467698792730X-RAY DIFFRACTION99.9652415711
2.2366-2.35450.2260451439731330.1858769131482725X-RAY DIFFRACTION99.9300699301
2.3545-2.50190.2352994658921520.1804898907452729X-RAY DIFFRACTION99.7921718046
2.5019-2.69510.2169367757971520.1815134462782724X-RAY DIFFRACTION99.9305072967
2.6951-2.96620.2390476718261450.17405218022741X-RAY DIFFRACTION100
2.9662-3.39520.1838159917951470.1694667157842720X-RAY DIFFRACTION99.7911590672
3.3952-4.27680.18183530431480.1602030125432750X-RAY DIFFRACTION99.8277643817
4.2768-39.19070.1938333159051480.188100977582774X-RAY DIFFRACTION99.3201903467
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04272576764360.2255930956030.4076332065668.380492673990.4804730783524.23889455835-0.100551470516-1.16694040784-0.7563197328411.251398299360.4439775495630.6345409021860.7193256669510.336479928734-0.2616881341240.3557221279160.0315297168051-0.05927376873590.6120077730060.3296390742510.464562722839-21.86526193322.478079680816.3286526741
25.181565146270.997983788706-1.262498527753.77181047174-0.4058170844523.078956680720.249550929101-0.733083587463-0.3684410570260.306003740031-0.265310978797-0.3166289433080.2785026831590.3455819365260.0246200195570.148228369865-0.0246482797557-0.06551920520830.2279589154750.08472552407290.270155853814-20.72802967176.6983277883310.1674185624
31.05810111405-0.7332828506160.7754142106421.599934270970.7853243569652.182262269420.11675890248-0.274768721672-0.01744276739490.0758330380125-0.134334833374-0.230779596894-0.01949030222730.130535385385-0.02056374657980.0832409515775-0.0282599091589-0.02623728437320.1764462184030.0215558509540.159989930897-20.744239642212.55822010516.65973633621
41.765719409340.3115530372910.3480711292583.131318144380.05336272272473.568081043290.125860728138-0.492279589997-0.2066278232120.419480738528-0.276599221818-0.4552162303650.1983370655750.414735081386-0.06050182461940.240920808432-0.141538375619-0.1272576424780.4770911636330.1234475165090.145341449802-18.200868376615.574705802615.9633557299
52.429849298681.52426787810.2436008086512.905672850780.549048037542.0497827203-0.0320029604073-0.04479275752860.167808381529-0.259694684617-0.01556929102510.0554164523422-0.2626458458170.0301545976870.03913017030870.125781187363-0.0147089493772-0.005800684145380.0858728657298-0.0001734400352710.10142736389-27.735087367218.8799038579-0.652495036008
61.86048484609-0.3194110792321.342786036642.423836376860.03287616177972.381316480520.0300453600294-0.257378823818-0.216004068697-0.2855871908330.018919046524-0.06449891036220.101315098396-0.0658953519727-0.04719718111090.1044839816810.00397385533980.0234043905020.100252462392-0.009370356580390.140898924845-28.22740897923.89102129526-1.14371240826
76.390079519180.738575689621-1.503800537142.63693055616-0.1502827929834.58985115618-0.08371620340850.535341296995-0.341784349544-0.7111117505840.25017322548-0.29738745195-0.02183442500680.0859303820291-0.08447865543430.280593793748-0.043682841740.03068910258020.115892336673-0.04991544331240.134030818722-31.42896956793.43543641905-11.9133930612
81.98854076273-0.0783225464623-1.054449322340.44569930672-0.07030651194172.07382802424-0.170345878006-0.0414065392479-0.519114981045-0.39993641320.0393430896562-0.7556048049260.2626810638960.4076622646570.1952636908720.1263576741120.01521203769790.1537702684750.160969167463-0.0457753869010.392081206364-20.86688059051.30783601097-2.28004802808
99.508246481091.430822449951.344116676364.45364780452-0.04925970756724.318646549430.229037975284-0.0217201420739-0.13482287363-0.1382129103640.0111121750352-0.09794314687410.111317072307-0.141447643475-0.2415307812410.144513150911-0.0151383544373-0.0004892432553050.06691335558660.002915487798470.11548341833-35.0140363139-4.24888496638-5.0679441048
103.5243359662-0.2517110034860.2392214353485.98792915296-1.404526176020.338788785639-0.305390600547-0.3596522994070.749085233428-0.577074623030.239460229658-1.22131047973-0.7163493801151.11373716484-0.1137569134850.439278107289-0.281592553251-0.04620746193940.544143167434-0.01194329100070.431275219825-31.4400628811-3.5995048606927.4401583894
112.828192540450.163776217808-0.7082067655593.77100068491-1.111859973776.470795721170.00420678977488-0.1528788339430.2370779276060.294799442208-0.309432140282-0.305055994115-0.3726434763880.7314010299190.163400190290.219497888823-0.0733610709684-0.0634210115380.2374265958780.0351929653240.158161120676-37.3594020593-7.8243676307629.401284453
122.26590929608-0.7286252199820.5713265838131.895035758960.9378779616850.904267299713-0.0124394118655-0.1657150421350.02154334646850.271854514112-0.162054418245-0.130706880155-0.03441642803510.3366431502970.2118237702560.145313987992-0.0232602372456-0.03714072195340.1970322318480.03926754715450.0961223349693-40.8703192794-13.68124309529.8871815275
132.35166473393-1.012797626650.4096190447512.96393091165-1.466336080892.473028321110.050000330947-0.0643842442955-0.1970600386920.0482791265632-0.06914845670860.1447828279070.05951227639230.185519895634-0.008359107240780.0956790464494-0.00829894966560.002703273959080.1028212759120.01904660227830.106700969354-46.4318364065-19.574977710425.0145077261
142.60849959932-0.08748976435851.306062060472.586626795560.4582035489021.24532482786-0.03686933632020.0895945975570.0910176110330.09682529965560.04066522296130.162122257108-0.2513256739660.1959581749870.01398308375960.143573792946-0.002127269835420.02278542012670.0909224689962-0.01248323007340.0933327911164-49.7830421428-5.3240799696323.6093139316
152.410989137070.0143955000011-0.1775984011061.67254432508-0.09242340733523.18966169899-0.156403132918-0.2270555691740.09430905490970.5088253636050.1552654235920.494341845689-0.387882855523-0.172737921655-0.0001886954523780.2439626199820.04487386325320.07534184628480.09813161373640.007137500032350.189901513397-55.355545151-3.5003830950626.4072213574
164.515320213470.08800923467661.379092504324.34189382435-1.454240727462.27875516209-0.2296756404480.05348853699190.1079020316420.2171119463730.0572075712420.180661651274-0.103859733968-0.1251885873270.189910454540.1443914643230.006407483472590.002748250680010.06897243732490.01293399162590.148216363585-54.57279442943.1955320740517.4264347804
1700-0000-7440.7861302511037.166091-129947.996503000122383.197273-7812.825435857440.786130250.160370504495-0.01403931026860.01248972738470.177012723765-0.01888515822350.174403022963-34.94396878319.968252725733.19045367544
18000000-3069.32427823106442.3407875828.6158011-104954.1835613069.32427823-3007.317727160000.232740240873-0.01290643527450.0191839810560.2415495364640.01835007905210.219412213194-32.46993160917.531755415544.9328739085
190000000000000000.8492672763870.00465887082593-0.1864848544650.5313922555860.07638522916810.998667668947-32.19710120910.4252463990488.65773606317
200-005.86851313689E-120025608.7055885278364.086821-21795.3027092-369079.671005-25608.705564-145599.089874-2.25415537408E-597016.9570699-2.44755067823E-50.6215160688560.07527003900360.1714462944510.479165128641-0.07032989562920.633751265344-30.8532671546-0.7248504076486.7002056413
210000-0000016730.6366168-14862.6481034-10042.074888129869.4133798106289.66330214862.64810340.731239719975-0.2548398087240.3786414701420.544519290005-0.2869418791230.982443971028-22.6726471229-9.61874229439-4.76399884386
224.382818887943.50254622863-1.254971751163.57598482431-2.325937231922.612286708420.103894615435-1.888335846810.4734271058371.763400085030.380648783381.53156118119-0.621336584446-1.38593807846-0.2708537156980.530335356771-0.008443936216370.2022064327410.72296720822-0.03131185515830.366450931465-36.95483788198.337330151288.41416914681
231.999993085552.000000947661.999999686621.99999541721-8.609059352521.999995307255.076119586090.658886319823-5.272185678152.33015250016-3.452094066613.469104162047.042846687490.632441068897-1.625483261430.617910153458-0.108661153017-0.2298305968150.68060725558-0.2592300184120.585209082403-15.287150425722.73767336611.2830861092
24001.1995814614E-12000-77384.1757421-24275.5647461392105.3867240-00-602245.588317-54069.712537977384.17574211.04448919730.20165527064-0.2958893656350.421459406331-0.08511932688830.62930363142-35.69383300377.37752855287-13.248266032
25000000-2658.5308773643667.93532721085.11464382-46799.2661572658.53087736-1426.150674750000.595789453969-0.05621531022240.001298350642120.5872384217140.01082186116570.482903489544-12.990535107721.0078375856-0.771279221938
261.99999756742.238483197999.747725904412.410778193994.093484072281.9999983833318.4684915036-28.329640342145.6004873677-9.1479828614526.5923456091-61.1472409126-23.362532113134.3736813584-45.04507940720.936528286497-0.2246630178570.0846749163120.651237832841-0.04348954636820.996273222702-15.627672939522.6260609938-7.20659816461
27000000-013099.702359-0-13099.702359-0-00000.1683195372550.01471232923770.01296376175960.1723133915530.0200405984580.162490342644-46.324275425-11.077994113516.3112360884
280-001.42560820394E-1100-1.5731267148E-83.21401888848E-956111.53949236.29250685919E-8-1.28560755518E-8-224446.157969-56111.5395095224446.1579742.85873427003E-80.219108089589-0.01335213520688.99304183696E-50.2179669564030.009597852417790.219662213045-44.2623267841-8.6430544571818.5223429485
290000000000000001.00367469952-0.00520350309024-0.2304253198220.5723684123370.0459628667910.722206624646-40.4143479007-1.5574135032318.1773437584
3000-00003212.71442761-3861.8455091821144.6908486000-16567.8322973-36.8163896961-3212.714427610.52218624027-0.01515308198560.1970652476540.630944546719-0.1981797599380.626276052919-42.1483086426-0.30199797182219.8754825098
310000-00-0001317.22062359282.31397899254124.9489854-379.675306789-54366.3680055-282.3139789920.88564965442-0.0567006178594-0.4796358332940.3884265351390.02017025192460.770662258764-27.0083925122-4.910417551439.26576497528
326.861293371685.51286027784-4.832743554438.56069174827-2.566558947093.82344644082-0.3297011127911.28346671311-1.16137553758-1.0104817230.202152161833-1.649149142921.270531754011.967849240930.1678927697930.4867255697010.1860631338150.104888237890.721761762016-0.03842576967590.514765579658-41.0874735986-9.89091489714.3630529966
331.99999812251.99999544596-7.423810829221.999996273522.000000206331.99999310392-1.71643560822-4.170998382228.85301878558-3.89409177703-3.44806698071-4.47165468256-4.518236133760.7385403720815.177809231350.5102633279110.273295328683-0.170593134080.5539896739630.02151747286470.815021830755-35.5194209675-23.934248213834.4719583624
340001.92191648767E-901.10466316946E-10000124013.10213339684.1926763-3099537.79775-91273.64316951781526.54889-39684.19267630.626143550465-0.0189006684654-0.03603968728350.413570489339-0.009686272153310.692649911574-62.7731144116-8.4143950946817.8409393788
350001.433E-101.0E-112.23E-10000196436.753777-81600.62118922310944.7029460518.3938374-3595720.4404581600.62118920.527016199838-0.02278017976240.05412077335440.758271457839-0.02472314431060.432768792271-47.0721610548-22.221939287338.5830001833
361.960514533662.33576441912-0.02990156120088.047038155513.939293793963.3509946998151.6354988321-77.365129772965.730080490815.5414702206-9.584337932219.78994699137-61.793913130871.2496966187-42.04540510470.809381065411-0.1051473338560.1567324988651.06960236447-0.1098918710861.10331875577-49.30096059934.362061700561.33505058086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 201 )
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 238 )
7X-RAY DIFFRACTION7chain 'A' and (resid 239 through 252 )
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 279 )
9X-RAY DIFFRACTION9chain 'A' and (resid 280 through 296 )
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 42 )
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 63 )
12X-RAY DIFFRACTION12chain 'B' and (resid 64 through 88 )
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 200 )
14X-RAY DIFFRACTION14chain 'B' and (resid 201 through 238 )
15X-RAY DIFFRACTION15chain 'B' and (resid 239 through 279 )
16X-RAY DIFFRACTION16chain 'B' and (resid 280 through 296 )
17X-RAY DIFFRACTION17chain 'A' and resid 401
18X-RAY DIFFRACTION18chain 'A' and resid 402
19X-RAY DIFFRACTION19chain 'A' and resid 403
20X-RAY DIFFRACTION20chain 'A' and resid 404
21X-RAY DIFFRACTION21chain 'A' and resid 405
22X-RAY DIFFRACTION22chain 'A' and resid 406
23X-RAY DIFFRACTION23chain 'A' and resid 407
24X-RAY DIFFRACTION24chain 'A' and resid 408
25X-RAY DIFFRACTION25chain 'A' and resid 409
26X-RAY DIFFRACTION26chain 'A' and resid 410
27X-RAY DIFFRACTION27chain 'B' and resid 401
28X-RAY DIFFRACTION28chain 'B' and resid 402n
29X-RAY DIFFRACTION29chain 'A' and resid 411
30X-RAY DIFFRACTION30chain 'B' and resid 403
31X-RAY DIFFRACTION31chain 'A' and resid 412
32X-RAY DIFFRACTION32chain 'B' and resid 404
33X-RAY DIFFRACTION33chain 'B' and resid 405
34X-RAY DIFFRACTION34chain 'B' and resid 406
35X-RAY DIFFRACTION35chain 'B' and resid 407
36X-RAY DIFFRACTION36chain 'B' and resid 408

+
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