[English] 日本語
Yorodumi
- PDB-7yto: The Crystal Structure Analysis of Creatine Amidinohydrolase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yto
TitleThe Crystal Structure Analysis of Creatine Amidinohydrolase from Alcaligenes sp. KS-85
ComponentsCreatine amidinohydrolase
KeywordsHYDROLASE / E.C.3.5.3.3 / Hydrolyzes creatine / sarcosine and urea
Function / homologycreatinase activity / Creatinase, C-terminal / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Creatine amidinohydrolase
Function and homology information
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 Å
AuthorsChen, R.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770846 China
CitationJournal: J.Phys.Chem.B / Year: 2023
Title: Creatinase: Using Increased Entropy to Improve the Activity and Thermostability.
Authors: Jiang, F. / Bian, J. / Liu, H. / Li, S. / Bai, X. / Zheng, L. / Jin, S. / Liu, Z. / Yang, G.Y. / Hong, L.
History
DepositionAug 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Creatine amidinohydrolase
E: Creatine amidinohydrolase
F: Creatine amidinohydrolase
A: Creatine amidinohydrolase
B: Creatine amidinohydrolase
C: Creatine amidinohydrolase


Theoretical massNumber of molelcules
Total (without water)276,2346
Polymers276,2346
Non-polymers00
Water3,531196
1
D: Creatine amidinohydrolase
E: Creatine amidinohydrolase


Theoretical massNumber of molelcules
Total (without water)92,0782
Polymers92,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-34 kcal/mol
Surface area27240 Å2
MethodPISA
2
F: Creatine amidinohydrolase

F: Creatine amidinohydrolase


Theoretical massNumber of molelcules
Total (without water)92,0782
Polymers92,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area7050 Å2
ΔGint-34 kcal/mol
Surface area27110 Å2
MethodPISA
3
A: Creatine amidinohydrolase
B: Creatine amidinohydrolase


Theoretical massNumber of molelcules
Total (without water)92,0782
Polymers92,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-37 kcal/mol
Surface area27110 Å2
MethodPISA
4
C: Creatine amidinohydrolase

C: Creatine amidinohydrolase


Theoretical massNumber of molelcules
Total (without water)92,0782
Polymers92,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7580 Å2
ΔGint-34 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.946, 113.761, 111.482
Angle α, β, γ (deg.)90.000, 94.903, 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

#1: Protein
Creatine amidinohydrolase


Mass: 46038.973 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHU9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15%(w/v) PEG 6000, 100mM Citric acid/Sodium hydroxide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.31→40 Å / Num. obs: 105747 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.26 Å2 / Rsym value: 0.071 / Net I/σ(I): 3
Reflection shellResolution: 2.31→2.35 Å / Num. unique obs: 5251 / Rsym value: 0.718

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.31→40 Å / SU ML: 0.3157 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.4248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 2005 1.9 %
Rwork0.2147 103694 -
obs0.2155 105699 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.07 Å2
Refinement stepCycle: LAST / Resolution: 2.31→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19156 0 0 196 19352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219639
X-RAY DIFFRACTIONf_angle_d0.484426599
X-RAY DIFFRACTIONf_chiral_restr0.04182776
X-RAY DIFFRACTIONf_plane_restr0.00313481
X-RAY DIFFRACTIONf_dihedral_angle_d19.28957135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.37X-RAY DIFFRACTION
2.37-2.43X-RAY DIFFRACTION
2.43-2.51X-RAY DIFFRACTION
2.51-2.59X-RAY DIFFRACTION
2.59-2.68X-RAY DIFFRACTION
2.68-2.79X-RAY DIFFRACTION
2.79-2.91X-RAY DIFFRACTION
2.91-3.07X-RAY DIFFRACTION
3.07-3.26X-RAY DIFFRACTION
3.26-3.51X-RAY DIFFRACTION
3.51-3.86X-RAY DIFFRACTION
3.86-4.42X-RAY DIFFRACTION
4.42-5.57X-RAY DIFFRACTION
5.57-35.750.22921350.18077534X-RAY DIFFRACTION99.26
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)
11.206481694981.43434588544-0.3219230822833.465485457320.4833849262262.096362665970.621258924791-0.879786197811-0.1014973375181.15696303495-0.722862604098-0.536744532980.377937300003-0.4897379494240.006620591163010.980144836735-0.434052342539-0.05351753027380.9525818762430.1019703364990.244972722518-37.65969166744.07697570636-37.8487764713
20.794993206381-0.3267473637381.488122041541.35010450478-1.130167419913.028179267570.212752029623-0.910128112604-0.00849604175980.686179485488-0.263476337288-0.396120307973-0.517621382572-0.375481608325-0.3128269744451.09993811398-0.664458352753-0.223548927621.082794693860.3164856075190.382150633502-34.70922371720.436946007135-35.4267814512
32.575010884350.2914822417160.5653318474572.179915720120.5677319123910.2883945405390.646075914564-0.467515366138-0.9527868777260.971078443844-0.725515786518-0.5100722775090.215388279492-0.407186207605-0.0134277966931.06024520229-0.576750833538-0.1114817431391.059711672970.1428114440440.38992294617-40.476611066-6.54112780806-40.7869935531
42.144771031611.398596326740.07365648557643.21135270772-0.5793631898231.076481634320.286180050133-0.2626884097280.04473431388040.632275105699-0.32324800314-0.2098568632380.108783892693-0.5729956298380.003938111257640.497609680646-0.1729819556920.05390364903730.569163524735-0.03266516309240.200465733752-32.642608871714.1741176372-48.9342428487
53.764712738770.1184933675992.615940295392.71308434942.178948228484.058667110630.296240076404-0.07613756046710.0759385105656-0.194329281433-0.187289272642-0.589305098841-0.155966873459-0.37466692041-0.06547972931420.2927338768550.02321548976530.04835134780060.3218695806330.09953259095030.508480680386-22.692248486318.7007139055-60.5352261765
62.746711979930.554364999928-0.2675094971893.88725074338-0.4953985114213.003152821750.3545863962480.09009557206250.4098884806450.012869489974-0.2918995129420.372279952464-0.521716899106-0.899957128218-0.06202145049440.5110089257490.2021093980830.1246550823330.5998483656870.01485244374320.394369955739-37.776478429527.268118553-60.9952837729
73.088671609730.5653990734110.1047042834623.40944469802-0.09797492212123.019714578990.220315137769-0.118326685110.6004962069840.1921384026-0.3356724016130.127718619108-0.507468570135-0.4915288227610.08753446859740.5904664030290.1979004833480.1540097177040.4389433049510.005879614222360.45204714054-34.002888779530.4360454679-58.8587452033
82.14299345380.475229825618-0.5190761951137.040674155280.8766656733392.936406219860.1731851513780.166884273689-0.119123665716-0.347293785649-0.0936491447679-0.1080535512510.0471560001269-0.634171904679-0.05699475851380.2967076818760.0117258177530.03720560429570.5912036039910.02714021054250.216474705872-34.58264262980.668963458351-74.0391236065
93.538302707570.5436522965090.7125145345056.314727539990.4405946746534.230350366450.1607046385250.285644104047-0.133109092286-0.331664619406-0.107739905520.093360738688-0.21131073392-0.579583777175-0.02606266754170.3178805484510.1042377523320.1082529439430.6157109038270.0935661361910.293956877648-37.22414785446.44441250079-69.1001414354
103.177565757891.96056049346-0.2521144458485.17412691912-1.23664075072.05381382066-0.05220779664390.491597224490.204819683020.2490023970440.08593037063320.394239159582-0.157168477415-0.757688065313-0.02089496767960.3200827975960.0898199817480.06154667389060.815342471040.02356208321530.258243753092-42.93724350786.10384020888-70.4467261534
110.3894279954830.605604476289-0.1270798658892.539111367750.8407741752481.597375907460.516893261621-0.309028698906-0.5229866997040.636832324728-0.213420954564-1.043903124580.361868040119-0.315364429248-0.1516546184340.528595509678-0.13098403622-0.2574257571290.4188078217220.2368758377490.807869983161-18.5159327568-0.586027346165-53.2743519467
120.9966945656951.2013030074-0.5033489192331.54313879377-0.3539354364591.18397591190.122941434461-0.334816124847-0.4369879474080.982839625071-0.681741438369-0.308076341630.4503566890070.3876715404040.03407695184421.21181186891-0.354043024817-0.5267072937960.2205993523310.4655927617681.57010946006-19.1801081939-23.0039923371-47.8800224337
130.596467504937-0.400560100811-0.166906735030.464723403413-0.4142509988621.932050946340.490846586931-0.245931369391-0.7377104279410.844144745104-0.373206778408-0.7659770657820.552992929205-0.171151078316-0.3547879742480.924020707233-0.30836785056-0.4349859711070.4773276909690.2928438068850.958573505526-22.0649321414-11.6818348633-48.2883156875
141.688904471070.1720518821280.4032400127410.375498564215-0.6647223235031.521677698690.102685855894-0.190980530069-0.8589193365460.817284393884-0.219755371868-1.15529927890.5889222945950.21404791127-0.6369086298950.744253556571-0.0366892145337-0.6375127187040.2758925302070.4507084930241.56289568275-8.15068067363-8.77553660563-51.9302106497
152.384940414861.57596586564-0.4855298844525.52158407505-1.471798381494.48567404231-0.342271914977-0.9659754891010.4388514985260.559926011238-0.08607102024370.0649953306895-0.357411143027-0.2942481434650.4158301957670.625578677620.170675222984-0.1986372996420.763931378552-0.1146360079160.591768765445-89.615214244418.0315437229-36.3572617451
168.44020806360.5627006665612.377796190515.234670679730.8179574776354.75674417662-0.319169058567-0.7295139870270.1946213688430.409972911181-0.4907777903310.863137423353-0.783375246612-1.095767425210.751803716090.5042939348540.172307380245-0.05143060432940.744901848748-0.09323346674150.584218422942-96.564981454415.3255962069-40.0984298088
173.337600480050.04105871234330.7896103941151.1709544634-0.01021646590923.74092820881-0.62057314306-0.3322629691950.2009801990480.1419018389550.01089945818080.115405671879-0.8417119904410.09670276420310.5651489844580.5734440787910.0203768535951-0.187684952560.6315841025440.056340478510.705160953931-89.603959495914.0530072781-46.6584776625
183.12734118840.2158345640982.345870319071.50089888541-1.382037489183.34345823353-0.2295332081670.439936405773-0.584390333055-0.1391458441220.244355857999-0.070483460596-0.1536158677680.740290066382-0.05156370411040.352353119288-0.03247555022360.1365383807130.584902440183-0.03752619916610.827066952151-85.570985499-1.56754615733-61.9298987091
194.06324068666-1.43474770662-1.119280863351.1060485520.04821547118022.95564487383-0.3902380563280.610631956363-0.00647850523697-0.136471689326-0.000352279564995-0.416405062773-0.1257808670291.386012318710.3166076641420.434304642973-0.1103687639880.01206227538521.199374348080.1030968910490.738800063262-70.77168493757.29762719347-62.0936059906
203.68495366008-0.8396063567140.5549995268823.23472081544-0.9039451683682.370365269570.1080299645060.604609781868-1.09249477141-0.4646798875030.149231322565-1.008730728870.3244459745331.4499017726-0.2752893440770.5127259460250.2174295073060.1697072445641.003212262560.01124600971690.808542564591-67.4928102409-4.02872480919-56.597376291
212.781340074080.2466508210550.3702169292531.504355227760.2361127631061.174612697740.02487756026240.175444757602-0.026606986113-0.0428283760337-0.1104948235890.198813620953-0.0586042484897-0.01227192057280.08386256736920.3846038615490.08775304077830.04834658153910.2493676261980.01732308139360.241672590728-59.333354201410.78893413459.91309793087
220.7020708177660.49710863291-0.3087036254792.695432350991.835587204962.782697482190.01386847492150.605330684187-0.709192807401-0.2533696731940.000794752987109-0.1523738271140.227453786370.123575248433-0.04334409868380.5627944673240.134660009026-0.02653448688640.536081833853-0.2724542509870.707311517855-55.919681515-10.3721423023-5.16536764008
232.001903384250.2659264585360.4711924126233.57168002201-1.080762431472.37248996410.1150841267850.8405599957880.0757230821155-0.728955973599-0.154797925547-0.00973092934719-0.202943067849-0.1683102999490.05492251298570.6654801743860.212846305540.01781921459570.920998561170.09243935202060.305945137786-58.133236094117.4707544829-19.2910017847
242.037650281640.6430919669550.08400007448953.58460935252-0.7846435364287.381238316190.156736580331.56307338281-0.249937662282-0.565959856054-0.127164769559-0.2452074983060.4749354759280.248905646373-0.03024058649390.6484198072460.216108643774-0.02357229087710.984943943018-0.08687337441760.352031117864-55.31889280758.92090238738-15.8804603663
251.94828882392.534250063680.0401699172247.77415859073-4.196722286818.209817212830.1265649907950.989008789544-0.284815231178-0.591348263091-0.24300844356-0.8649833636620.1957424556910.3367668506960.04670606850150.508004955770.2031527286340.04655286369680.950756949220.07919276988240.33916008931-45.042191290316.2638377882-13.3840533068
262.69901025638-0.0628758724539-0.2163343620161.152817685270.02154003191920.9775328011090.06492021826970.544381956423-0.0138058430401-0.235566204166-0.1684335241830.33139116868-0.0112779951932-0.05731434735820.1012420618790.4128862259430.127750201978-0.06279991700310.461761943306-0.04520760384290.384536707401-71.146154124815.7058829265-1.96715557139
273.65819188718-0.192860211045-1.455886321682.183671272520.5817031877522.944210175550.07418518432720.2857576893270.636710070669-0.0595261291488-0.07337762233170.323638328055-0.372526536078-0.212468056154-0.02559201895640.3823664592830.127118788553-0.02894913858710.3956162860010.03964241066710.507534882996-76.202532519729.33147309686.27600454322
283.282953025111.16680729196-1.091898836263.565665547650.2735351319433.450321353440.1247091711770.6658217742090.867630623885-0.2345798753670.0006436334706231.13841094604-0.261217308874-0.830905106366-0.1631666398640.40003694620.209669220831-0.03406967842050.660989187440.00312511136410.781153989495-85.057606722326.3330001351.66901201066
293.49267625991-0.287892951812-0.3448619304953.98021620151-0.06384313156032.50422488450.10221160161-0.7983814905560.2668540259920.4858466399480.1004816785990.080755499856-0.3047406066370.208641896622-0.1886160490850.4334118640820.02456809262750.1121564827780.536135124355-0.04847933571720.27239318766-2.700289338550.24585124916119.175361509
302.463734462931.603487066731.170402778665.46443744331-0.9110594489522.373288212180.0238267590456-0.169321205211-0.03809065368780.4775764698560.169864570902-0.302114871381-0.1546487567190.312055988206-0.1827228827090.3094881970980.04259371434880.09041145389760.485538640955-0.07888991555010.2933718370385.20963079345-2.3782174661115.0058025266
311.375699779870.0312978609993-0.2138446002892.1610373344-0.4193095579142.099054748020.1177552536370.1070614548420.4975992058510.004426792384420.1302349554870.14883695377-0.534124246949-0.241302416673-0.2552235666710.3843993992740.07963773758270.1471530835030.4103336935290.04493050904660.48960439645-9.1607434422614.24975164840.544115627558
323.913977457591.19371802319-0.4814671481663.9111143498-0.9978683930613.4194291340.01912785554880.06769805019390.0276724780393-0.3931042799360.2822849723120.837582119358-0.441740926553-1.23110470382-0.311161358860.4717216022320.2243335671590.0226842606730.9075701078550.1960268464870.748399287642-30.16890342829.9131516056-9.44643606882
332.89569112364-0.009522648839020.393382128272.636200092320.2028316062713.04843233628-0.02177413697250.5152380779060.356259196968-0.2631090436260.07410053490430.428333386726-0.248826006159-0.631752870086-0.06360299374950.3528770494590.1300481415760.08661256267970.6290331931220.1593757955920.516204647932-19.62253490397.3634365414-5.48978530705
343.186363738672.49923250847-1.54472540632.79872138048-0.1181163635253.527757355910.07146750885470.233383324410.723368249386-0.2125572956090.2502713024111.2508664967-0.862090169793-0.974052479802-0.2993624099030.6727433846480.371798487120.1635704050760.6149940136950.1654017442961.01885504733-25.214392791822.3182897487-1.3471551214
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 4 through 68 )DA4 - 681 - 65
22chain 'D' and (resid 69 through 92 )DA69 - 9266 - 89
33chain 'D' and (resid 93 through 130 )DA93 - 13090 - 127
44chain 'D' and (resid 131 through 210 )DA131 - 210128 - 207
55chain 'D' and (resid 211 through 245 )DA211 - 245208 - 242
66chain 'D' and (resid 246 through 348 )DA246 - 348243 - 345
77chain 'D' and (resid 349 through 404 )DA349 - 404346 - 401
88chain 'E' and (resid 4 through 57 )EC4 - 571 - 54
99chain 'E' and (resid 58 through 85 )EC58 - 8555 - 82
1010chain 'E' and (resid 86 through 130 )EC86 - 13083 - 127
1111chain 'E' and (resid 131 through 292 )EC131 - 292128 - 289
1212chain 'E' and (resid 293 through 312 )EC293 - 312290 - 309
1313chain 'E' and (resid 313 through 371 )EC313 - 371310 - 368
1414chain 'E' and (resid 372 through 404 )EC372 - 404369 - 401
1515chain 'F' and (resid 4 through 57 )FD4 - 571 - 54
1616chain 'F' and (resid 58 through 92 )FD58 - 9255 - 89
1717chain 'F' and (resid 93 through 210 )FD93 - 21090 - 207
1818chain 'F' and (resid 211 through 245 )FD211 - 245208 - 242
1919chain 'F' and (resid 246 through 381 )FD246 - 381243 - 378
2020chain 'F' and (resid 382 through 404 )FD382 - 404379 - 400
2121chain 'A' and (resid 4 through 245 )AE4 - 2451 - 242
2222chain 'A' and (resid 246 through 404 )AE246 - 404243 - 401
2323chain 'B' and (resid 5 through 57 )BF5 - 571 - 53
2424chain 'B' and (resid 58 through 104 )BF58 - 10454 - 100
2525chain 'B' and (resid 105 through 130 )BF105 - 130101 - 126
2626chain 'B' and (resid 131 through 245 )BF131 - 245127 - 241
2727chain 'B' and (resid 246 through 371 )BF246 - 371242 - 367
2828chain 'B' and (resid 372 through 404 )BF372 - 404368 - 400
2929chain 'C' and (resid 4 through 57 )CG4 - 571 - 54
3030chain 'C' and (resid 58 through 130 )CG58 - 13055 - 127
3131chain 'C' and (resid 131 through 272 )CG131 - 272128 - 269
3232chain 'C' and (resid 273 through 313 )CG273 - 313270 - 310
3333chain 'C' and (resid 314 through 382 )CG314 - 382311 - 379
3434chain 'C' and (resid 383 through 404 )CG383 - 404380 - 401

+
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