[English] 日本語
Yorodumi
- PDB-8db0: Crystal structure of DMATS1 prenyltransferase in complex with L-T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8db0
TitleCrystal structure of DMATS1 prenyltransferase in complex with L-Trp and DMSPP
ComponentsDimethylallyltryptophan synthase 1
KeywordsTRANSFERASE / prenyltransferase / fungal protein / DMATS
Function / homology
Function and homology information


4-O-dimethylallyl-L-tyrosine synthase / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / alkaloid metabolic process
Similarity search - Function
Aromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / TRYPTOPHAN / Dimethylallyltryptophan synthase 1
Similarity search - Component
Biological speciesFusarium fujikuroi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsEaton, S.A. / Ronnebaum, T.A. / Roose, B.W. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structural Basis of Substrate Promiscuity and Catalysis by the Reverse Prenyltransferase N -Dimethylallyl-l-tryptophan Synthase from Fusarium fujikuroi .
Authors: Eaton, S.A. / Ronnebaum, T.A. / Roose, B.W. / Christianson, D.W.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimethylallyltryptophan synthase 1
B: Dimethylallyltryptophan synthase 1
C: Dimethylallyltryptophan synthase 1
D: Dimethylallyltryptophan synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,13912
Polymers189,3654
Non-polymers1,7748
Water8,215456
1
A: Dimethylallyltryptophan synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9163
Polymers47,3411
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dimethylallyltryptophan synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8083
Polymers47,3411
Non-polymers4662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dimethylallyltryptophan synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8704
Polymers47,3411
Non-polymers5283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dimethylallyltryptophan synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5462
Polymers47,3411
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.500, 108.400, 182.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain 'A' and (resid 11 through 13 or (resid 14...AA11 - 15611 - 156
12GLYGLYSERSER(chain 'A' and (resid 11 through 13 or (resid 14...AA170 - 211170 - 211
13LEULEUTHRTHR(chain 'A' and (resid 11 through 13 or (resid 14...AA216 - 271216 - 271
14ARGARGPROPRO(chain 'A' and (resid 11 through 13 or (resid 14...AA276 - 307276 - 307
15HISHISASPASP(chain 'A' and (resid 11 through 13 or (resid 14...AA311 - 321311 - 321
16GLNGLNALAALA(chain 'A' and (resid 11 through 13 or (resid 14...AA327 - 411327 - 411
21SERSERPROPRO(chain 'B' and (resid 11 through 13 or (resid 14...BB11 - 15611 - 156
22GLYGLYSERSER(chain 'B' and (resid 11 through 13 or (resid 14...BB170 - 211170 - 211
23LEULEUTHRTHR(chain 'B' and (resid 11 through 13 or (resid 14...BB216 - 271216 - 271
24ARGARGPROPRO(chain 'B' and (resid 11 through 13 or (resid 14...BB276 - 307276 - 307
25HISHISASPASP(chain 'B' and (resid 11 through 13 or (resid 14...BB311 - 321311 - 321
26GLNGLNALAALA(chain 'B' and (resid 11 through 13 or (resid 14...BB327 - 411327 - 411
31SERSERPROPRO(chain 'C' and (resid 11 through 24 or (resid 25...CC11 - 15611 - 156
32GLYGLYSERSER(chain 'C' and (resid 11 through 24 or (resid 25...CC170 - 211170 - 211
33LEULEUTHRTHR(chain 'C' and (resid 11 through 24 or (resid 25...CC216 - 271216 - 271
34ARGARGPROPRO(chain 'C' and (resid 11 through 24 or (resid 25...CC276 - 307276 - 307
35HISHISASPASP(chain 'C' and (resid 11 through 24 or (resid 25...CC311 - 321311 - 321
36GLNGLNALAALA(chain 'C' and (resid 11 through 24 or (resid 25...CC327 - 411327 - 411
41SERSERPROPRO(chain 'D' and (resid 11 through 72 or (resid 73...DD11 - 15611 - 156
42GLYGLYSERSER(chain 'D' and (resid 11 through 72 or (resid 73...DD170 - 211170 - 211
43LEULEUTHRTHR(chain 'D' and (resid 11 through 72 or (resid 73...DD216 - 271216 - 271
44ARGARGPROPRO(chain 'D' and (resid 11 through 72 or (resid 73...DD276 - 307276 - 307
45HISHISASPASP(chain 'D' and (resid 11 through 72 or (resid 73...DD311 - 321311 - 321
46GLNGLNALAALA(chain 'D' and (resid 11 through 72 or (resid 73...DD327 - 411327 - 411

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Dimethylallyltryptophan synthase 1 / DMATS 1 / DMATS1 biosynthesis cluster protein DMATS1


Mass: 47341.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium fujikuroi (fungus) / Gene: DMATS1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: S0EH60, Transferases; Transferring alkyl or aryl groups, other than methyl groups

-
Non-polymers , 5 types, 464 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 7.5 mg/mL protein, 0.1 M Tris-HCl (pH 8.9), 0.55 M NaCl, 25% (v/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.26→93.14 Å / Num. obs: 84491 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 39.58 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.079 / Net I/σ(I): 7.4
Reflection shellResolution: 2.26→2.3 Å / Rmerge(I) obs: 2.19 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4417 / CC1/2: 0.52 / Rpim(I) all: 1.26 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 2.26→93.14 Å / SU ML: 0.2561 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7039 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 2000 2.37 %
Rwork0.2062 157835 -
obs0.2068 84364 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.23 Å2
Refinement stepCycle: LAST / Resolution: 2.26→93.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11903 0 117 456 12476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004712385
X-RAY DIFFRACTIONf_angle_d0.77816959
X-RAY DIFFRACTIONf_chiral_restr0.05171852
X-RAY DIFFRACTIONf_plane_restr0.00542175
X-RAY DIFFRACTIONf_dihedral_angle_d18.87134246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.27671380.29365721X-RAY DIFFRACTION99.22
2.29-2.320.33131430.28095933X-RAY DIFFRACTION99.79
2.32-2.350.31971410.28395807X-RAY DIFFRACTION99.6
2.35-2.380.32051410.28375822X-RAY DIFFRACTION99.9
2.38-2.420.27521420.26435871X-RAY DIFFRACTION99.87
2.42-2.460.28411420.26085844X-RAY DIFFRACTION99.88
2.46-2.50.29731470.25175854X-RAY DIFFRACTION99.97
2.5-2.540.26551400.25735836X-RAY DIFFRACTION99.83
2.54-2.590.29671430.25385874X-RAY DIFFRACTION99.85
2.59-2.640.27771440.24945844X-RAY DIFFRACTION99.83
2.64-2.690.30711390.25495807X-RAY DIFFRACTION99.75
2.69-2.750.28251450.25245858X-RAY DIFFRACTION99.65
2.75-2.810.28321440.24515862X-RAY DIFFRACTION99.78
2.81-2.880.28541440.24425822X-RAY DIFFRACTION99.47
2.88-2.960.22611400.23365790X-RAY DIFFRACTION99.81
2.96-3.050.26921430.2215901X-RAY DIFFRACTION99.98
3.05-3.150.24721410.22475835X-RAY DIFFRACTION99.93
3.15-3.260.25841440.21725868X-RAY DIFFRACTION99.97
3.26-3.390.26131460.21055861X-RAY DIFFRACTION99.92
3.39-3.540.20631360.19125855X-RAY DIFFRACTION99.9
3.54-3.730.20691420.18515865X-RAY DIFFRACTION99.93
3.73-3.960.20941410.18155847X-RAY DIFFRACTION99.95
3.96-4.270.17781380.16845853X-RAY DIFFRACTION99.65
4.27-4.70.18841320.15115872X-RAY DIFFRACTION99.88
4.7-5.380.18081450.16215825X-RAY DIFFRACTION99.92
5.38-6.780.24991370.20585882X-RAY DIFFRACTION99.95
6.78-93.140.18891340.18915826X-RAY DIFFRACTION99.62
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)
13.26198924322-0.0846038567501-1.479603945072.4784538479-0.3506153774362.640296640150.0494933575859-0.08561514164560.07346604634920.1253897030160.03635827549570.363880734092-0.214182333054-0.0854516210011-0.1040632089060.2652225755620.03787014026660.02157321417240.2477372455690.08524127418320.23465042713318.1946614567-2.61441861497-16.0069229985
28.61240759864-0.4259483806443.629964290952.793937437252.504612774497.1344510138-0.1001594940890.257191388588-1.0505275578-0.05127379214040.04338497184031.167298594-0.0547082550964-0.5306274039050.1422533465050.2888170229390.002638841877870.04053920836040.4619253521450.006654235712150.7888491927283.94186826883-17.4786086085-18.6257460891
33.928495318230.998322206564-0.2593430599255.040410952140.3538956436932.58305901932-0.2428430470170.302715759472-1.19207999078-0.188090386553-0.00407666285150.6403584231770.446256630216-0.6191881402690.2560892472910.27082830749-0.03563246052820.06075156430180.386566013672-0.01241282816950.81588252911610.0052661467-20.659195348-19.7186418365
41.40999275083-0.891246042857-1.742662849556.734535223421.313048744851.88195972114-0.6516119563360.312343222816-2.09443350482-0.240936049740.1357228869260.5034913132320.723703077928-1.236632288250.4048829003270.525203512799-0.2232543578130.2869119226810.235404862578-0.04170184797511.4776709620413.9585645398-32.8973227965-22.6265685808
54.788663770190.230518010076-2.551667960292.50651720860.4765105179881.46004514447-0.3184637269190.408677799366-1.4537421712-0.281671543194-0.2162839693580.4281849320.441351158945-0.1004881582380.4838511774570.410363314760.01889665216980.07085595287810.317212616731-0.05930765433830.66287344582626.4533269619-29.3175554464-24.1608937433
62.523319027360.0139285214338-1.002678584854.148153209211.489836901914.37310763641-0.351283945258-0.134736609257-0.845570100820.0726014007602-0.06607951745680.03250268915330.492554315770.1732687459550.3873868585220.2921781163110.04620196415750.1399925416670.2908461800890.1651305570970.53583459803128.7203581052-27.8412190704-16.9618547236
73.53042131755-0.597145373934-0.6172927982223.408505576750.1350890840190.340088875251-0.0856101765834-0.0706540111055-0.05149078298020.09672132295020.00818739128217-0.114473580077-0.01892730980340.2280100895460.05094447186640.2315678350970.02629774785180.02205848095290.3480208503580.1170151113060.20008977003834.4724095209-13.4929725409-18.5912166323
83.48067790298-0.9711214927891.207597578312.703730561690.2567274015012.511217496290.05676993444780.09147173965290.0670946095929-0.178286907109-0.005600042642810.178294801758-0.0677902153281-0.099051797455-0.0461640270140.193319406847-0.03064032410590.01935068020710.193969057392-0.01533354731060.21932196375320.336603171239.2888313891-77.2394778521
94.5669825591-0.999438661990.435597322498.92647881301-1.484677719684.27682878458-0.0223520263744-0.1581308303540.402019890934-0.3178654745860.2296806432950.692465001223-0.514397610406-0.425369375764-0.1318204980770.234618813821-0.007628721356950.02333365258610.286145927084-0.04703308525410.37478579849413.523964167452.1638248937-77.0729006542
104.083680012380.01145747648491.141565506288.097666346111.073271392652.71814459716-0.247586701416-0.3188186162521.42502400940.434994878788-0.0005399637427910.619728862689-0.917919693988-0.4230411228690.2216449502920.5195229456230.120787606267-0.06997828812010.374092720688-0.1145539617150.7213032591813.373009518866.8467760325-72.4752125438
115.50132833673-0.4031595457481.085564553532.065844293010.5382966377960.456534969759-0.272725996301-0.4029770290411.033782816850.1259265509880.0433704003064-0.347674059624-0.4918627023870.03961885679680.1861533194190.524618672424-0.0110830447397-0.03687728173110.372609064283-0.1514054765660.64318827809428.086632704564.44611149-68.7385167095
129.04205961332-1.06974879974-1.405957390886.771995293572.527646001434.6610184210.07052294336290.3861622618471.16633834822-0.6201537510470.125812526933-0.210529827553-0.907097261590.16702159922-0.1583412204970.516457379463-0.0367680741119-0.08464576422470.258297321011-0.01812253108450.54062411211730.956448314262.9246234258-74.92082224
135.83254510463-0.03939224531550.5866829369545.47496326883-1.033864701832.49537878727-0.232267892720.2284106793430.103538244044-0.2948040002520.243578297099-0.169701648309-0.1148999539170.2803589302270.00985701150040.193959051662-0.0600397100814-0.006849794555660.254136001425-0.04637084096210.25852254356637.846857724449.6037426618-73.1060879779
142.33866420494-0.4105518651470.1403576676845.379699412970.9441165849892.934422701360.261884186122-0.0743899559183-0.1638489813660.185921383862-0.03257986390380.4709752997630.560603741911-0.347273101688-0.2260009258040.432965455606-0.0755695314465-0.07545590476340.3194676461120.1100192207280.32022662526218.65951083337.89230445154-69.4404466908
153.98444414984-0.450655972728-1.999892070517.75994368195-1.803390088031.734633529990.3361450809510.0238864469165-0.400722949289-0.0859250338773-0.0193409778566-0.1131459095621.29352386247-0.0197877650996-0.3486167819240.830276663183-0.00811241951817-0.2783989884370.4338567399140.08408797709090.42788080820122.6690969814-5.43690370632-73.9866247352
163.76312797957-1.344389931780.8554738808763.80641461006-2.528824477863.434289244750.695990209719-0.111403359356-1.76031553493-1.08320107878-0.451859252004-0.6299903128731.489722821570.662945664566-0.1813850958381.617639859490.28484723961-0.5017085418930.297347125132-0.04604164328031.1013026571331.467395683-19.2644141082-72.6093552402
170.367577583398-0.7984060069760.922383402742.82325354847-0.5849522300382.472266865970.358320399889-0.870256513917-1.237724352770.341874116249-0.0710406308882-0.03977999165231.04112320155-0.154709974399-0.3306085052741.08678693696-0.193364928027-0.4013836249490.89359265610.4752832329160.94483254174927.149155604-14.7998424302-56.1353161377
182.70521103933-1.61510840112-0.1529146804863.6569307572-0.9669528666874.064397041270.761106057752-0.385737887321-0.3334232240560.683210686791-0.3125819752-0.05373821239320.841691827902-0.134829490688-0.1785376949311.23730685244-0.325931695304-0.4994608369850.7066775489450.444593014620.55813220564225.196571063-10.8370339024-57.632504333
191.52387643564-1.335799252461.419675365873.95111521582-1.068611748343.927866209950.258563597866-1.7366185214-0.6154473055710.6143645565920.5041622916470.4519831490370.218514708613-0.564195320446-0.6608713241370.789190966056-0.166688299574-0.1142782364381.035212379360.279361406330.48441810999721.20042368731.33424227339-50.0458006242
202.18017432760.2016560512260.9033521336245.16325175783-1.026521739851.5168860550.369221385824-0.1520838851730.2963623737060.5170448651630.2097343964071.27994733132-0.179341043967-0.508691883884-0.6231668056070.7353470104850.04599179989230.240513455630.5526066617020.3239505541310.98345508058912.957362146525.4131520151-28.9181000479
212.782482334440.03706437722650.2956747879614.0081912012-0.1649651329121.250961117550.493227455499-0.4997809830171.077700582761.44708021523-0.09140550152610.201433487499-1.110714496680.313218359779-0.4194065227021.51755527652-0.08353681485180.4513739451710.559554073254-0.02128028844221.0552219566222.019675790443.58609748-20.6488778953
222.36706337930.71938870356-0.8081637032644.74200682248-1.962082588644.377105724050.1884103463230.6833971505891.04135795697-0.2175291408430.572533724621.19254551479-0.393742464995-0.0533687978505-0.6933804177650.7634740359920.05832973686710.212009999520.6570784488360.3589022663350.98131379055822.937377342341.6434925257-42.8723972825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 243 )
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 294 )
6X-RAY DIFFRACTION6chain 'A' and (resid 295 through 343 )
7X-RAY DIFFRACTION7chain 'A' and (resid 344 through 414 )
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 199 )
10X-RAY DIFFRACTION10chain 'B' and (resid 200 through 243 )
11X-RAY DIFFRACTION11chain 'B' and (resid 244 through 294 )
12X-RAY DIFFRACTION12chain 'B' and (resid 295 through 343 )
13X-RAY DIFFRACTION13chain 'B' and (resid 344 through 412 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 153 )
15X-RAY DIFFRACTION15chain 'C' and (resid 154 through 199 )
16X-RAY DIFFRACTION16chain 'C' and (resid 200 through 227 )
17X-RAY DIFFRACTION17chain 'C' and (resid 228 through 315 )
18X-RAY DIFFRACTION18chain 'C' and (resid 316 through 343 )
19X-RAY DIFFRACTION19chain 'C' and (resid 344 through 412 )
20X-RAY DIFFRACTION20chain 'D' and (resid 11 through 124 )
21X-RAY DIFFRACTION21chain 'D' and (resid 125 through 262 )
22X-RAY DIFFRACTION22chain 'D' and (resid 263 through 412 )

+
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