[English] 日本語
Yorodumi
- PDB-6u1v: Crystal structure of acyl-ACP/acyl-CoA dehydrogenase from allylma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u1v
TitleCrystal structure of acyl-ACP/acyl-CoA dehydrogenase from allylmalonyl-CoA and FK506 biosynthesis, TcsD
ComponentsAcyl-CoA dehydrogenase domain-containing protein
KeywordsOXIDOREDUCTASE / ACAD / FK506 / allylmalonyl-CoA
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase domain-containing protein
Similarity search - Component
Biological speciesStreptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBlake-Hedges, J.M. / Pereira, J.H. / Barajas, J.F. / Adams, P.D. / Keasling, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2020
Title: Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase.
Authors: Blake-Hedges, J.M. / Pereira, J.H. / Cruz-Morales, P. / Thompson, M.G. / Barajas, J.F. / Chen, J. / Krishna, R.N. / Chan, L.J.G. / Nimlos, D. / Alonso-Martinez, C. / Baidoo, E.E.K. / Chen, Y. ...Authors: Blake-Hedges, J.M. / Pereira, J.H. / Cruz-Morales, P. / Thompson, M.G. / Barajas, J.F. / Chen, J. / Krishna, R.N. / Chan, L.J.G. / Nimlos, D. / Alonso-Martinez, C. / Baidoo, E.E.K. / Chen, Y. / Gin, J.W. / Katz, L. / Petzold, C.J. / Adams, P.D. / Keasling, J.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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: Acyl-CoA dehydrogenase domain-containing protein
B: Acyl-CoA dehydrogenase domain-containing protein
C: Acyl-CoA dehydrogenase domain-containing protein
D: Acyl-CoA dehydrogenase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4248
Polymers169,2744
Non-polymers3,1504
Water26,2841459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19680 Å2
ΔGint-114 kcal/mol
Surface area50550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.520, 100.060, 148.510
Angle α, β, γ (deg.)90.000, 100.310, 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
Acyl-CoA dehydrogenase domain-containing protein / acyl-CoA dehydrogenase TcsD


Mass: 42318.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993) (bacteria)
Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Gene: STSU_32075 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I2MTW3, Oxidoreductases
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1459 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 4, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→68.4 Å / Num. obs: 196484 / % possible obs: 97.65 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1119 / Rpim(I) all: 0.06086 / Rrim(I) all: 0.1277 / Net I/σ(I): 8.99
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.063 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 19281 / CC1/2: 0.524 / Rpim(I) all: 0.5664 / % possible all: 96.41

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UKW
Resolution: 1.75→68.4 Å / SU ML: 0.2006 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9074
RfactorNum. reflection% reflection
Rfree0.1787 9864 5.02 %
Rwork0.1462 --
obs0.1478 196467 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11965 0 0 1459 13424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012312213
X-RAY DIFFRACTIONf_angle_d1.043716562
X-RAY DIFFRACTIONf_chiral_restr0.06471870
X-RAY DIFFRACTIONf_plane_restr0.00662119
X-RAY DIFFRACTIONf_dihedral_angle_d5.9179203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.32063296120X-RAY DIFFRACTION96.31
1.77-1.790.32873236164X-RAY DIFFRACTION96.48
1.79-1.810.29063515994X-RAY DIFFRACTION96.43
1.81-1.840.29943406155X-RAY DIFFRACTION96.59
1.84-1.860.25213186119X-RAY DIFFRACTION96.56
1.86-1.890.28473316154X-RAY DIFFRACTION96.79
1.89-1.910.2533536096X-RAY DIFFRACTION96.9
1.91-1.940.24253206181X-RAY DIFFRACTION96.78
1.94-1.970.24593556110X-RAY DIFFRACTION97.01
1.97-20.23113356179X-RAY DIFFRACTION97.22
2-2.040.20943556154X-RAY DIFFRACTION97.11
2.04-2.070.20493046141X-RAY DIFFRACTION97.21
2.07-2.110.20513126238X-RAY DIFFRACTION97.4
2.11-2.160.18023066197X-RAY DIFFRACTION97.55
2.16-2.20.1643276219X-RAY DIFFRACTION97.67
2.2-2.260.18763396214X-RAY DIFFRACTION97.67
2.26-2.310.15973216227X-RAY DIFFRACTION97.83
2.31-2.380.16283406213X-RAY DIFFRACTION97.89
2.38-2.440.17243676200X-RAY DIFFRACTION98.07
2.44-2.520.16572986263X-RAY DIFFRACTION98.04
2.52-2.610.15173366240X-RAY DIFFRACTION98.16
2.61-2.720.16923106292X-RAY DIFFRACTION98.2
2.72-2.840.16573566256X-RAY DIFFRACTION98.44
2.84-2.990.16353260.13036292X-RAY DIFFRACTION98.63
2.99-3.180.16113710.12616259X-RAY DIFFRACTION98.53
3.18-3.430.16573330.12946289X-RAY DIFFRACTION98.66
3.43-3.770.14072840.12136337X-RAY DIFFRACTION98.57
3.77-4.320.11813090.11166383X-RAY DIFFRACTION98.67
4.32-5.440.14333060.11746415X-RAY DIFFRACTION99.07
5.44-68.40.19413090.17266502X-RAY DIFFRACTION98.91
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)
16.82833501053-0.2617846284470.9729068576384.24042648872-4.295021433144.46915767726-0.07989540048160.282518089126-0.706511885888-0.734912288337-0.211156125662-0.6611168203540.6754097666380.1977114627710.4010349815520.2693393642870.03652708965540.07868953202470.261715873874-0.06883444027630.28842192545246.0936205061-16.333494107414.7221237017
22.21678381579-1.05202483567-0.5524642196112.2047920676-0.9287135321961.573378142280.09553470323880.3614335708470.0418648910346-0.332513831204-0.1494932562580.05257520815820.0493660582769-0.02553685967240.01379307299660.229215698920.02257137666460.01723360800030.269692939238-0.03001111849780.1507903602437.4607578117-5.351521146737.35304869291
32.552934927460.233652410252-0.8251958428390.699055718449-0.3538151044691.74837256099-0.09251682740790.0929619836655-0.345001432286-0.0642150063220.0124440935990.03730558392360.203010724548-0.0839794490160.08529512300090.154421518238-0.001805920145850.01398066407660.126387590348-0.03927081527660.17259606109130.315803971-16.04639043121.3027275284
43.762187458930.311417399295-0.03930639672091.054580620750.8025641931252.33826760793-0.0445550729371-0.0287780090382-0.001776383939330.0177979299612-0.1130097228790.2638296863-0.00310266497028-0.3556670774090.1551361015150.115948330045-0.000245270422894-0.006869450154670.177547605323-0.01546660825630.15462853441214.2237548534-3.2885868015324.5308197466
51.805931860990.479655735837-1.074810307610.601087520188-0.4633445350141.293096883-0.02470760364520.221231023201-0.103318730125-0.07131361225320.002772628277720.09712576075070.0351088221709-0.2400741398050.02430049072230.126331653428-0.00651114580779-0.01953027075690.198981533193-0.04566754333070.14201589786315.4866578652-4.8295006385419.3109896754
67.839765088553.7907688564-2.358304399682.3136743506-1.315155408551.32277671264-0.02361547947210.18873937562-0.141640299149-0.0570504616099-0.00512980116621-0.0739280125722-0.0279578909744-0.03334961246190.08640817399680.1062267007090.00518578124931-0.005303102652850.121343169078-0.01242391152270.088274752663340.8158393868-2.7639921019525.6628709477
76.350145420473.63736447072-1.811720108412.6191953355-1.284655742281.269400729460.04528548301990.0131176976019-0.1584086299420.0241029281473-0.0826140051426-0.153755778122-0.05389025658410.04314348600260.1016972562510.1226378470650.0159209812480.004291017145290.114057283066-0.004192421479610.10762518594652.3751490153-0.27936739982229.4246574054
82.658474802920.764311188757-0.5579491297260.191285615933-0.1292917163111.026061366440.0777342370783-0.254110774136-0.1718470825730.116443806861-0.1021148271060.000780860853335-0.00343294102116-0.0009832323992250.009897691252730.09967201794180.0141148077746-0.001417766000640.141422111769-0.005927383149710.13285018283535.3703327986-4.5431188952634.359504109
94.065684623852.37697325295-1.948083642262.04821591744-1.370557233541.95338534984-0.1192407943270.175147777404-0.148672340238-0.1613748800470.0117212111718-0.08927275861910.010124785972-0.05635507558330.1136970613080.1738334523630.0111172255452-0.004230715462450.155683616134-0.005919888352970.14516690596942.84161603768.2561892565818.8242514492
101.988160794080.4186441145323.314769669824.460557845610.9973861091016.710812609750.129692896365-0.404268629925-0.1698355885360.652830402882-0.102808816327-0.1685208602280.494805298306-0.151364604223-0.08421688100510.1883068766910.00870677556698-0.001617909481650.2240214666450.002561704960310.16836555455130.09776028950.45948577360547.3171572265
111.89272935624-0.278907376874-0.06125477337362.590017199360.857205153451.60953950343-0.0384274691324-0.125474682139-0.1833197708170.20409345376-0.0509085209510.1295270284650.147545272346-0.1381308503630.1036854675650.160485106245-0.02949014940910.03024909333470.1725380725460.0411842830060.15635583436551.7260110064-8.8718757388761.842734291
123.03054211853-1.63027652102-1.461877723252.688416984111.419522090672.80670480019-0.0610736634839-0.0563966975911-0.2416402487930.0510331303373-0.0257407191924-0.1010427747050.2212220877480.16702903870.07276607065140.129454706753-0.02990960066130.0103139754510.1323246659530.03652221935610.18291912383266.6787942802-13.212514609357.3833862213
135.485470691360.191549743471.013935522070.148308572247-0.7046247697883.95530149603-0.08864166759650.3837196199040.008615766077380.0359780564639-0.113756485963-0.203092141147-0.07074988738270.5112290106830.1578208727280.13979643356-0.02505674302320.02079748588210.1735944932120.007277938950540.18111348931579.0565871628-0.030121198145449.4152765125
142.6297039401-0.422223982434-1.070577914580.7956077500750.4148927186761.60316296745-0.037260330509-0.166852377098-0.08889481598850.0475071616259-0.0129497276457-0.0927923587421-0.0181036268880.166650950560.04494023030420.1377348701-0.0177720633562-0.01288757213920.1805601210760.02773773789770.14803938327377.350446884-2.6769522175756.3935508447
151.03090915268-0.1211109591240.1001611163940.3059883253120.05390899827580.451510282985-0.00267722956587-0.0229931908975-0.06342222065460.0149264101567-0.02815589411770.0157269409181-0.006130346476370.0005376215685880.03257483848890.147398360525-0.01271053404870.01446000669330.1355769878940.01916958048750.14297329735652.2977660091-0.044394028505650.701755699
161.55344437147-0.158931328744-0.1525480664090.06529418685730.2037326566571.012314687240.05766200631760.190833078363-0.226388510429-0.102100933585-0.08715403979840.05220955970320.01877129980090.0637541410330.012552666470.129166709782-0.009667205876230.01264902291380.1813889913510.002134913410370.17324842895856.0315905133-3.961489143741.8734706241
172.07360219047-1.00651126333-0.4909714483811.490977487460.6673340109930.857195711309-0.0807257610019-0.088666545267-0.09384958487810.183471344722-0.02300700495680.09974285776730.009776093839010.07589587182320.08785599735880.179298650407-0.004576093108830.003993638738020.147415876240.009570856989730.15010451419348.489115322111.230642789755.1078606469
187.278138755540.01480507618363.479371393743.668021642-0.9119558072767.645633382340.1063579959390.687465911978-0.344815228642-0.5599977627770.09816602967030.04784677222520.3654529909910.503248939133-0.2049003441930.170699072745-0.014659939680.002923241678230.2297071728840.005693844253610.15110966545161.1215243369-1.2374812314227.4678001345
190.8894726089852.49202618638-0.4549752386219.73151598477-1.07450319830.247817514497-0.1114519956470.1436593190440.6815324041440.18585201251-0.121286268590.785602139665-0.47141691573-0.2695543119640.1678892441760.3004298962970.075850560705-0.03212048382680.2727812572630.02376327433810.31218452505131.450573179441.522261267914.9903164547
201.944960804070.2579052396040.09225748684861.079905926760.02959447492451.24479362936-0.08872702486220.2568383625970.25829853913-0.03946588088710.0199139079513-0.00705377039178-0.270270591032-0.009127443205710.04290108264920.290273975049-0.00565763609978-0.04416924231010.1925538512050.06648731597340.16703482074344.212141757237.9310064589.52930165449
211.878628331050.185153215082-0.9972760362492.12402035392-1.027150718763.02454693325-0.04612145249580.2150113871440.0542852400016-0.0847337288878-0.140374067317-0.23832152813-0.1002184836610.3291055864670.1697428232650.213119721583-0.0415148834131-0.007501465688960.2789296685910.07409938280890.17633803658561.570215084329.03598687193.1697162672
220.6947712035770.102099704459-0.2007452295570.347490607157-0.1781165364180.819431868989-0.01113324439870.04603037044830.0859557238726-0.0223408509178-0.0364523768252-0.0225684186666-0.1904486427410.07444125727780.03420895031430.193179691125-0.0117238082285-0.02691026956710.1263528019240.02000431732870.13713363251444.288084242227.300201714121.9139529922
238.60636121271.480611142290.4490585804285.50367920397-1.058630262653.49052328899-0.11953871082-0.08340728653560.2909565307990.140648407731-0.0421677224874-0.16441053448-0.3474361216810.2066604367760.1682186917010.21672275997-0.02512535021460.002370268756030.1717936849970.05262524292630.15569746678862.806705453527.077097354530.5863908455
243.36908129397-4.04711784954.323412498535.11416198347-5.991845271138.05469044237-0.2120743299960.07447571336180.7821203267660.1561861139-0.309239891465-1.01444371296-0.6329670739820.258383954480.5157010300810.293606379821-0.0572917258336-0.0106181307780.1988408542660.00583290570660.32987722239360.353785339944.411452309253.2936092805
252.18174067519-0.467509975058-0.1694033013771.281313748750.07545389721581.323518946450.00795119559203-0.09697781633530.202176624699-0.023624796666-0.03104313293520.00960482895306-0.2581898641740.01857535755760.02956719497010.223776378389-0.029867442901-0.02383870102770.12223147613-0.02589130484940.13926193075447.540506357841.906888315759.1722637345
262.163761194450.344497108364-0.3940865125151.666844420310.4477116240692.862095752550.0673036629459-0.03189367517720.2070239928870.183211054488-0.1278698292760.362486683371-0.09134483394-0.220052636890.05474302766160.1736285739580.02810953294940.02650941463670.144616819487-0.05452134373960.19528104017231.439306549834.383512407966.6230500377
272.01361181514-1.132713309870.8178203141363.30435895659-0.4677913829153.05433626209-0.0334629638626-0.240121704283-0.02177323952580.0676248157449-0.08372487081970.387835729298-0.151206635705-0.4607066934670.02387659759050.1390947912680.02041028101270.01902520471080.238768323923-0.07530700654370.18582312478229.145315307535.795694391468.3324184885
281.52165722348-0.387655255249-0.3136340532271.482487419520.1297026938021.534573767230.0176844657869-0.1777092768460.1437796881060.0889782002321-0.07548606309420.220353278648-0.148493266877-0.1282049361510.05844947883860.172423082084-0.01474033343140.006464527506020.168245347194-0.07201206329460.17465435494235.527568293933.452226320667.4224591143
291.94948893127-1.12601277887-0.7963041425241.096534813710.6346344553790.9951307795060.0249984764032-0.02432851189890.0653699627949-0.0700688343626-0.0555247502598-0.00889503540789-0.2064151145370.02734249251750.009389836375230.190899373056-0.0313015882995-0.02744649976970.09994260781620.01414511227660.13287962621252.897961501329.679867910542.8398707211
302.15801444866-0.679661113996-0.2873595999650.2882817712710.3380738094881.112115155950.1345906439310.1300310211860.155847944888-0.301281068671-0.1240530965060.0668386627276-0.261086936658-0.164709048573-0.01835031150130.2179218908220.0106849457188-0.0323627804050.122767192758-0.005167416554110.15114284469239.494995058433.703139147344.1561345271
315.11824932162-2.428369810751.523980436261.76550199399-0.3968264133780.703988515319-0.118303318438-0.009070623489490.2461596299120.0338524734877-0.0211531232785-0.0640450916861-0.138577646621-0.05093874816490.1629854435450.192260771192-0.01181555339720.007478404992010.1240956700960.005703475426430.12731683168644.546186436223.03011721348.0932186644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 256 )
7X-RAY DIFFRACTION7chain 'A' and (resid 257 through 299 )
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 337 )
9X-RAY DIFFRACTION9chain 'A' and (resid 338 through 366 )
10X-RAY DIFFRACTION10chain 'A' and (resid 367 through 388 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 113 )
13X-RAY DIFFRACTION13chain 'B' and (resid 114 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 189 )
15X-RAY DIFFRACTION15chain 'B' and (resid 190 through 299 )
16X-RAY DIFFRACTION16chain 'B' and (resid 300 through 337 )
17X-RAY DIFFRACTION17chain 'B' and (resid 338 through 366 )
18X-RAY DIFFRACTION18chain 'B' and (resid 367 through 389 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 17 )
20X-RAY DIFFRACTION20chain 'C' and (resid 18 through 110 )
21X-RAY DIFFRACTION21chain 'C' and (resid 111 through 189 )
22X-RAY DIFFRACTION22chain 'C' and (resid 190 through 366 )
23X-RAY DIFFRACTION23chain 'C' and (resid 367 through 383 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 17 )
25X-RAY DIFFRACTION25chain 'D' and (resid 18 through 109 )
26X-RAY DIFFRACTION26chain 'D' and (resid 110 through 157 )
27X-RAY DIFFRACTION27chain 'D' and (resid 158 through 189 )
28X-RAY DIFFRACTION28chain 'D' and (resid 190 through 219 )
29X-RAY DIFFRACTION29chain 'D' and (resid 220 through 299 )
30X-RAY DIFFRACTION30chain 'D' and (resid 300 through 337 )
31X-RAY DIFFRACTION31chain 'D' and (resid 338 through 382 )

+
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