[English] 日本語
Yorodumi
- PDB-7pth: C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pth
TitleC54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline
ComponentsCholine sulfatase
KeywordsHYDROLASE / choline / sulfatase / sulfate
Function / homology
Function and homology information


choline-sulfatase / choline-sulfatase activity
Similarity search - Function
Choline-sulfatase / Choline sulfatase enzyme C-terminal domain / Choline sulfatase enzyme C terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
ACETATE ION / CHOLINE ION / DI(HYDROXYETHYL)ETHER / Choline sulfatase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116261GB-I00 Spain
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.
Authors: Gavira, J.A. / Camara-Artigas, A. / Neira, J.L. / Torres de Pinedo, J.M. / Sanchez, P. / Ortega, E. / Martinez-Rodriguez, S.
#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 Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choline sulfatase
B: Choline sulfatase
C: Choline sulfatase
D: Choline sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,90817
Polymers237,9824
Non-polymers92513
Water38,6062143
1
B: Choline sulfatase
D: Choline sulfatase
hetero molecules

C: Choline sulfatase
hetero molecules

A: Choline sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,90817
Polymers237,9824
Non-polymers92513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area21650 Å2
ΔGint-32 kcal/mol
Surface area65680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.773, 103.973, 108.966
Angle α, β, γ (deg.)90.000, 104.037, 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

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Choline sulfatase


Mass: 59495.551 Da / Num. of mol.: 4 / Mutation: C54S
Source method: isolated from a genetically manipulated source
Details: C54S mutant / Source: (gene. exp.) Rhizobium meliloti (bacteria) / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A410NSD4, choline-sulfatase

-
Non-polymers , 6 types, 2156 molecules

#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2143 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M TRIS hydrochloride pH 8.5 30% w/v Polyethylene glycol 4K

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.85→45.49 Å / Num. obs: 161235 / % possible obs: 93.5 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Rrim(I) all: 0.11 / Net I/σ(I): 9.6 / Num. measured all: 746171
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.884.71.1983790180980.6810.6151.3491.294.9
10.13-45.4940.036423610480.9980.020.04226.895.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.19-4092refinement
REFMAC5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G60
Resolution: 1.85→45.49 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2005 8007 4.98 %
Rwork0.1629 152919 -
obs0.1647 160926 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16572 0 55 2143 18770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007417480
X-RAY DIFFRACTIONf_angle_d0.881623835
X-RAY DIFFRACTIONf_chiral_restr0.05032469
X-RAY DIFFRACTIONf_plane_restr0.0093181
X-RAY DIFFRACTIONf_dihedral_angle_d6.01652417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.34012550.30855187X-RAY DIFFRACTION94.54
1.87-1.890.3552630.29745178X-RAY DIFFRACTION94.81
1.89-1.920.30112980.27955136X-RAY DIFFRACTION94.75
1.92-1.940.29913020.26935101X-RAY DIFFRACTION94.64
1.94-1.970.29223120.25195118X-RAY DIFFRACTION94.63
1.97-1.990.27162600.23655169X-RAY DIFFRACTION94.4
1.99-2.020.24172620.2255140X-RAY DIFFRACTION94.46
2.02-2.050.26892710.21245146X-RAY DIFFRACTION94.18
2.05-2.080.23592790.19675151X-RAY DIFFRACTION94.21
2.08-2.120.21822560.18525138X-RAY DIFFRACTION93.81
2.12-2.150.20852730.17965074X-RAY DIFFRACTION93.84
2.15-2.190.20782570.16645132X-RAY DIFFRACTION93.84
2.19-2.240.21372390.16155131X-RAY DIFFRACTION93.57
2.24-2.280.20262510.16095114X-RAY DIFFRACTION93.19
2.28-2.330.2162480.15925047X-RAY DIFFRACTION92.75
2.33-2.390.21892880.16035008X-RAY DIFFRACTION92.14
2.39-2.440.21262670.15584988X-RAY DIFFRACTION91.52
2.44-2.510.19552710.15354967X-RAY DIFFRACTION90.61
2.51-2.580.2112600.15724837X-RAY DIFFRACTION88.71
2.58-2.670.2142480.16324765X-RAY DIFFRACTION86.76
2.67-2.760.20652080.15934340X-RAY DIFFRACTION79.23
2.76-2.870.1831930.15623905X-RAY DIFFRACTION71.52
2.87-30.19062790.15835052X-RAY DIFFRACTION92.65
3-3.160.19012660.15355424X-RAY DIFFRACTION98.56
3.16-3.360.20652840.15125428X-RAY DIFFRACTION98.52
3.36-3.620.17732570.14295446X-RAY DIFFRACTION98.79
3.62-3.980.16522770.12655443X-RAY DIFFRACTION98.83
3.99-4.560.14292840.11955442X-RAY DIFFRACTION99
4.56-5.740.16222930.13365467X-RAY DIFFRACTION99.07
5.75-45.490.18783060.17835445X-RAY DIFFRACTION97.15
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)
11.748590351120.2096495848470.07333600052971.35729009295-0.3217255244021.50329430892-0.02128523265970.0769762331313-0.0844896928103-0.04110074160540.0306473081012-0.118255154670.05330103017620.208058627560.004515184554420.1661645454360.0368399345339-0.01639371302320.175596122659-0.02339031600270.164750986755-1.90166973893.95787648854-2.86870559588
20.622087594326-0.124596095431-0.07758886798460.62521725422-0.1463791063350.4868008767620.02922863124240.0554562580597-0.0223098289365-0.08335148603080.02187705305770.05496156250860.0563545009198-0.0574220269184-0.05221946565710.1871226558280.000723576236654-0.02136467774040.173401730664-0.004170715363420.180149184415-22.46490039856.28250683429-8.54512058394
30.564441668884-0.1970843962840.1933003212660.475211568208-0.3254654164961.038077869630.02022861203450.0309476022306-0.000179173006107-0.004914400709320.02790442310690.0135716676978-0.04703410265420.0116839469483-0.05882562015480.1729639983939.53419469518E-50.01065925488920.176490605024-0.007331771946180.176896478588-15.582205649214.68910888253.98961715423
40.728908024471-0.04111393627920.219023868380.614007458303-0.3658435089221.263331886450.01458888185050.06934944921350.0334400308326-0.03516442750210.00339857884222-0.058841675727-0.05487094432320.185747387032-0.007257645606710.1593043364030.003440724732980.02293527284930.187124534396-0.02339758996360.179599792881-5.79530954814.8157659261-3.20607030019
50.907049362739-0.211716986112-0.005557457907060.980841277686-0.5997445159851.092176365470.01083345819170.131219109208-0.207340403347-0.05912846006630.02081930611530.02672688450210.1858459489750.0815961423734-0.02140671343710.2449332840710.02722545089870.002012109795370.234054158796-0.05661885407760.245776310724-11.6984785263-0.0605023376234-16.2710899133
61.53577233437-0.0709202327506-0.7169664253810.3215023726850.1398209492281.117914906760.04608138208980.218788501524-0.043362598663-0.0762168765538-0.0348260028809-0.044879224123-0.0147293919029-0.005146214187140.003314945028410.2148302345440.0188242089972-0.008982980272660.184966310172-0.01245685114370.186688816217-17.348726345514.8791041024-22.049842394
72.41570822616-0.16937402332-0.7530859754281.341490667360.2216123995441.367110574710.01570242313310.0537102575711-0.4126890673220.000483635312352-0.04486883718980.01632009911580.2128236618510.0765705891558-0.02087738139160.264608758097-0.01643810897-0.05966905989690.2182419606610.01367825333590.251916313526-20.0080123873-13.188908841323.2566616786
81.260411606910.459036183855-0.1622984608011.36932466747-0.632338983160.956432629615-0.03442614155290.130879558569-0.105389146476-0.0703176369974-0.00202935167284-0.1912365189930.06835871407860.2317278109010.03986579959720.2149250128430.0421222645518-0.003616293287580.377191877799-0.03325585634770.260626288265-20.9504683634-47.2948408412-29.5967232391
90.421398617981-0.0134215909235-0.1480258013230.684451342042-0.2215652999690.5064611729550.03565741907250.09832647067260.0191625588111-0.05099281230510.0123237429186-0.0313931867160.02208962403570.0768116253167-0.04547516065660.1910679456790.0253089670582-0.01156226154930.278290295876-0.007019776992630.211663134139-41.2809859537-45.2656842957-35.0103725554
100.6314283785050.270308443412-0.1998173626070.94631449711-0.4728626489350.9877886087970.04607966798370.0656776381020.1303865033290.0137333748714-0.0092490268533-0.0325311886872-0.09447882514060.168738838645-0.01918799392680.1658036916280.00636060528499-0.002372812598810.265258261281-0.006198484923620.215523454066-29.6231076-34.8690510877-27.6631448505
110.460294271972-0.0527303049314-0.04147329644620.523685766175-0.09923643817560.6251388832940.02065992109190.1326642955550.0185887055384-0.0704258823020.0148665804587-0.08794237975990.03235016319910.153132688084-0.03144728595880.2035293062610.02915974494270.01314709283890.342021846896-0.01339884717740.238718068285-26.8064137797-44.1015315633-40.3972687465
122.97260279623-0.604481355567-2.294920719640.3332169399860.5846420811191.818541784310.1849730862050.481965565905-0.0592675421679-0.139950339108-0.121990552898-0.0021561004744-0.0894341823784-0.222814638003-0.06133445729390.252616571420.0477030671627-0.01636079769310.370061702567-0.005136930008840.226294498517-41.9068556724-36.7963646387-52.6117111148
130.08530021754920.1090548058370.1023465387880.688894783415-0.2620975191890.5490869654090.0602877237847-0.0108393858011-0.04444524973150.06325219349980.0209682229821-0.04202402040840.1281543086710.110926413227-0.06492934680270.2297928890420.0306202100875-0.03060412862780.238432212025-0.04259907030140.221170714169-43.8333017891-54.7912077656-9.91994246247
141.361222772710.3617930658660.3163465078751.589815812980.613111822861.06882942048-0.07366896935430.07368784099890.0370823228497-0.08987461554930.00665769506540.1908716993830.0170844560774-0.1644465534490.06867766322650.1735957959120.0098661821147-0.02640865933330.2422553712310.01073298443030.1680664804846.03521025922-43.1868708676-36.3409149027
150.2749952027530.0216635861720.0131501624780.217797948683-0.02686420043770.2548024595490.005207389573630.0574052509016-0.0476530670361-0.02255898618980.0183341698635-0.02587564721230.05985978811750.0118054419612-0.0232421403640.1945611878780.0109008906194-0.01951242057720.204987911534-0.01037774230490.18853289836623.8597871253-48.1789475314-34.0156555369
161.538451612951.05136385123-0.01870459879052.267266578130.1318147570971.041534008920.09781411211680.01323373287410.0249239909870.129688033754-0.07297846244490.07056567141310.029672721414-0.0115679351821-0.01829465480150.1565892573030.0134374782019-0.007207678058010.189744866772-0.0001152613701130.15760546474911.6320557689-45.2021813635-27.220328063
173.153411211030.282238346352-1.175998459630.757593125970.07345457906281.90891177989-0.06708242717360.275593838041-0.552731883395-0.0317072303272-0.0658209193329-0.01246884305870.342998289661-0.1627399661730.1523416207830.289021813957-0.0481447615847-0.04002547087150.23985689927-0.05627388415680.30445016521711.0900230997-68.1546008974-45.4347291166
180.364735649747-0.150134997773-0.07366233045010.4722856116260.09984302189510.5473805600570.02747849981610.12758970383-0.00506657374655-0.08599981047030.005706477017720.02375344523520.00752158217711-0.0134157223713-0.02895745189570.200999827610.00454852893489-0.03168625500220.2463414724340.00111833602930.1988626411213.3826317346-46.91718754-45.5757036257
191.41467636091-0.1046943928870.7462595842120.283817635429-0.3668385416321.48365119206-0.009250044758310.1643952328620.00370797223417-0.0116217518831-0.0124889857766-0.05429796242790.01227746706280.1678688567780.01283477725990.2228949167850.00274877005377-0.005376288513440.187043610398-0.0136318320810.21950499420231.9587213677-52.2419214746-44.2823263779
200.8861229140520.4619627604290.1811506096341.39397081666-0.3476262589211.70527468936-0.00583647762251-0.01261423310690.1764628730150.05487630024080.04724297758810.122596998869-0.237932366459-0.0877477835018-0.01024953529840.225667792480.01515123008540.04080238252760.1907871009140.01722383724050.23719461120514.7773877944-26.293972985-6.59700363776
210.235552668363-0.08726307781830.1007061539420.343163037347-0.1021066415980.4235244127010.02023943983840.01365506668940.01758699422920.004239505454080.0181619853801-0.01211726993060.03191089159960.0929772095632-0.04024477843540.1937772259790.0156815210686-0.02294914249820.237534292906-0.02821316856320.21481775155-39.3288373327-46.87063006057.84227329236
221.24787413796-0.12168536465-0.08992060014640.58302599605-0.04696101331950.8774607173590.0691244371914-0.0306722903981-0.110096306383-0.0322776858592-0.084775030541-0.08627059743260.1567945821360.2405764969970.04164912859330.2118539693080.0234206060017-0.04792547970180.261835537049-0.04799824414640.200828715359-29.9214357325-56.09708128689.48254738453
230.316461492294-0.01431905136530.1019221622470.302747986726-0.0007182813849590.4712539965130.0166608330935-0.06240584640050.007097463598020.06335154882230.0148262856796-0.02954520501410.006555572536820.0897967375361-0.02965735695040.2118805227470.0180062420028-0.02693750050770.24208510099-0.03247023612110.221195226032-35.8528544729-48.014616092220.7090737554
240.02169095057320.0151713563388-0.0379246072170.790695542845-0.0801253934420.4920857035690.01800869484380.06506798522770.0222267897397-0.06494596405830.0379044853371-0.0611768123116-0.03119008926870.0521048068161-0.0583621279780.2165710814950.0220282654891-0.006528728861620.212486986443-0.01204423023830.251345141353-43.3092025245-35.3456782541-14.3009162018
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 40 )AA4 - 401 - 37
22chain 'A' and (resid 41 through 135 )AA41 - 13538 - 132
33chain 'A' and (resid 136 through 182 )AA136 - 182133 - 179
44chain 'A' and (resid 183 through 313 )AA183 - 313180 - 310
55chain 'A' and (resid 314 through 391 )AA314 - 391311 - 388
66chain 'A' and (resid 392 through 487 )AA392 - 487389 - 484
77chain 'A' and (resid 488 through 518 )AA488 - 518485 - 515
88chain 'B' and (resid 4 through 40 )BE4 - 401 - 37
99chain 'B' and (resid 41 through 135 )BE41 - 13538 - 132
1010chain 'B' and (resid 136 through 251 )BE136 - 251133 - 248
1111chain 'B' and (resid 252 through 431 )BE252 - 431249 - 428
1212chain 'B' and (resid 432 through 472 )BE432 - 472429 - 469
1313chain 'B' and (resid 473 through 515 )BE473 - 515470 - 512
1414chain 'C' and (resid 4 through 40 )CK4 - 401 - 37
1515chain 'C' and (resid 41 through 182 )CK41 - 18238 - 179
1616chain 'C' and (resid 183 through 214 )CK183 - 214180 - 211
1717chain 'C' and (resid 215 through 251 )CK215 - 251212 - 248
1818chain 'C' and (resid 252 through 431 )CK252 - 431249 - 428
1919chain 'C' and (resid 432 through 487 )CK432 - 487429 - 484
2020chain 'C' and (resid 488 through 519 )CK488 - 519485 - 516
2121chain 'D' and (resid 4 through 182 )DQ4 - 1821 - 179
2222chain 'D' and (resid 183 through 251 )DQ183 - 251180 - 248
2323chain 'D' and (resid 252 through 472 )DQ252 - 472249 - 469
2424chain 'D' and (resid 473 through 515 )DQ473 - 515470 - 512

+
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