[English] 日本語
Yorodumi
- PDB-6xht: Crystal structure of S. aureus TarI in complex with CDP-ribitol (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xht
TitleCrystal structure of S. aureus TarI in complex with CDP-ribitol (space group P1211)
ComponentsRibitol-5-phosphate cytidylyltransferase 1
KeywordsTRANSFERASE / cytidylyltransferase
Function / homology
Function and homology information


D-ribitol-5-phosphate cytidylyltransferase / D-ribitol-5-phosphate cytidylyltransferase activity / poly(ribitol phosphate) teichoic acid biosynthetic process / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isoprenoid biosynthetic process / cell wall organization
Similarity search - Function
Ribitol-5-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
THIOCYANATE ION / CDP-ribitol / Ribitol-5-phosphate cytidylyltransferase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis.
Authors: Li, F.K.K. / Gale, R.T. / Petrotchenko, E.V. / Borchers, C.H. / Brown, E.D. / Strynadka, N.C.J.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
C: Ribitol-5-phosphate cytidylyltransferase 1
D: Ribitol-5-phosphate cytidylyltransferase 1
E: Ribitol-5-phosphate cytidylyltransferase 1
F: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,50719
Polymers174,7936
Non-polymers1,71413
Water25,7071427
1
A: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0347
Polymers58,2642
Non-polymers7705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-33 kcal/mol
Surface area19910 Å2
MethodPISA
2
C: Ribitol-5-phosphate cytidylyltransferase 1
D: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4976
Polymers58,2642
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-32 kcal/mol
Surface area20410 Å2
MethodPISA
3
E: Ribitol-5-phosphate cytidylyltransferase 1
F: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9766
Polymers58,2642
Non-polymers7124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.731, 138.598, 109.532
Angle α, β, γ (deg.)90.000, 96.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 11 or resid 18...
21(chain B and (resid 1 through 11 or resid 18...
31(chain C and (resid 1 through 11 or resid 18...
41(chain D and (resid 1 through 11 or resid 18...
51(chain E and (resid 1 through 19 or (resid 20...
61(chain F and (resid 1 through 11 or resid 18...

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
11METMETILEILE(chain A and (resid 1 through 11 or resid 18...AA1 - 111 - 11
12VALVALPROPRO(chain A and (resid 1 through 11 or resid 18...AA18 - 1918 - 19
13LEULEULEULEU(chain A and (resid 1 through 11 or resid 18...AA2020
14METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
15METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
16METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
17METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
21METMETILEILE(chain B and (resid 1 through 11 or resid 18...BB1 - 111 - 11
22VALVALLEULEU(chain B and (resid 1 through 11 or resid 18...BB18 - 2518 - 25
23ASPASPASPASP(chain B and (resid 1 through 11 or resid 18...BB2626
24METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
25METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
26METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
27METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
31METMETILEILE(chain C and (resid 1 through 11 or resid 18...CC1 - 111 - 11
32VALVALPROPRO(chain C and (resid 1 through 11 or resid 18...CC18 - 1918 - 19
33METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
34METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
35METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
36METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
37METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
38METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
41METMETILEILE(chain D and (resid 1 through 11 or resid 18...DD1 - 111 - 11
42VALVALPROPRO(chain D and (resid 1 through 11 or resid 18...DD18 - 1918 - 19
43METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
44METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
45METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
46METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
47METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
48METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
51METMETPROPRO(chain E and (resid 1 through 19 or (resid 20...EE1 - 191 - 19
52LEULEULEULEU(chain E and (resid 1 through 19 or (resid 20...EE2020
53METMETALAALA(chain E and (resid 1 through 19 or (resid 20...EE1 - 2361 - 236
61METMETILEILE(chain F and (resid 1 through 11 or resid 18...FF1 - 111 - 11
62VALVALPROPRO(chain F and (resid 1 through 11 or resid 18...FF18 - 1918 - 19
63METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
64METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
65METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
66METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
67METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
68METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236

-
Components

#1: Protein
Ribitol-5-phosphate cytidylyltransferase 1


Mass: 29132.209 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tarI, SAOUHSC_00225 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G1C0, D-ribitol-5-phosphate cytidylyltransferase
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-V2V / CDP-ribitol / [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate


Mass: 537.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1427 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.25 M sodium thiocyanate, 22.5% PEG3350, 50 mM CTP, 10 mM ribitol-5-phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50.649 Å / Num. obs: 133473 / % possible obs: 98.16 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rpim(I) all: 0.05645 / Net I/σ(I): 11.92
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 13181 / CC1/2: 0.602 / Rpim(I) all: 0.5751 / % possible all: 97.64

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JIS

4jis


Resolution: 1.8→50.649 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 6771 5.07 %
Rwork0.1697 126679 -
obs0.1715 133450 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.05 Å2 / Biso mean: 32.146 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 1.8→50.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10872 0 101 1427 12400
Biso mean--28.14 40.17 -
Num. residues----1407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4080X-RAY DIFFRACTION6.759TORSIONAL
12B4080X-RAY DIFFRACTION6.759TORSIONAL
13C4080X-RAY DIFFRACTION6.759TORSIONAL
14D4080X-RAY DIFFRACTION6.759TORSIONAL
15E4080X-RAY DIFFRACTION6.759TORSIONAL
16F4080X-RAY DIFFRACTION6.759TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.37052040.3445418798
1.8205-1.84190.33792210.3317419898
1.8419-1.86430.34732070.3091415898
1.8643-1.88790.31382170.286420197
1.8879-1.91280.32712240.2684422298
1.9128-1.9390.26992260.2402413397
1.939-1.96670.29852040.2326417898
1.9667-1.99610.28032160.2198422498
1.9961-2.02720.25242190.2139421198
2.0272-2.06050.23922390.2011417698
2.0605-2.0960.26042100.1997419597
2.096-2.13410.25272330.1944419598
2.1341-2.17520.23912300.192419998
2.1752-2.21960.24642490.1739416998
2.2196-2.26780.21122450.1664423398
2.2678-2.32060.20012220.1622418798
2.3206-2.37860.22022210.1685426299
2.3786-2.44290.2252460.172419998
2.4429-2.51480.21912320.1687428099
2.5148-2.5960.24392330.1694424399
2.596-2.68880.22622040.1806428099
2.6888-2.79640.22852290.1772425399
2.7964-2.92370.24722290.1775430599
2.9237-3.07780.23362250.1677423699
3.0778-3.27060.22772210.1599428999
3.2706-3.52310.19052080.1546424798
3.5231-3.87750.17262400.1396426699
3.8775-4.43830.17062350.127421598
4.4383-5.59060.16332380.1238426798
5.5906-50.6490.18132440.1467427198
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)
11.50420.3589-0.10022.29050.00992.70910.0652-0.1107-0.04910.128-0.0387-0.2366-0.05010.36910.00130.0926-0.00930.00060.1538-0.00550.1867.90590.874132.29
22.38370.334-0.19182.1107-0.59544.5384-0.05280.02290.2483-0.02390.0298-0.1407-0.410.27910.01350.1596-0.0227-0.00820.119-0.00140.20514.99519.967430.6183
37.3682-4.85814.87954.7907-5.96748.0394-0.01970.07240.02210.5994-0.11820.1395-0.4149-0.09090.12480.13690.0110.00020.137-0.02050.1197-8.12415.839127.8632
43.5482-1.67461.11722.3263-0.30962.26030.06290.11560.1594-0.3444-0.0886-0.134-0.12940.07950.02220.1755-0.0340.02740.12850.01120.14291.27650.059417.1417
50.4927-0.49010.23163.7193-1.6751.095-0.0497-0.0833-0.0429-0.11920.0275-0.00880.0421-0.05350.01850.1272-0.00210.00440.1917-0.00580.19610.8485-21.70725.2221
65.9340.3434-2.42236.2735-1.39595.53060.03840.10690.0904-0.0246-0.03950.6395-0.1193-0.55930.01150.13790.0028-0.04070.1783-0.04070.1694-11.6444-1.163721.097
74.64791.1692-6.64062.8248-1.28949.76850.1705-0.9934-0.30020.4284-0.19170.28610.1112-0.0899-0.04340.2376-0.060.02480.36720.02980.3095-12.9917-8.998928.6452
84.6015-0.39412.71312.49910.65554.51480.00750.026-0.0102-0.09180.038-0.04830.05420.0336-0.06050.1205-0.0110.02620.05460.01960.16622.7175-10.188121.1515
97.44055.2654-0.70598.3441-5.20924.7996-0.6525-0.0132-0.9925-0.2457-0.3757-2.28210.04860.29030.8810.2042-0.01410.0070.1979-0.00030.630219.1706-8.867631.5678
104.49341.9089-2.59746.4758-4.02638.89520.07580.5760.5352-0.7899-0.0738-0.2364-0.46260.36260.16260.30280.01780.05120.27730.09330.320821.167-34.72621.0822
113.40150.1966-0.02852.58980.16812.45460.05350.14290.3478-0.1494-0.0534-0.7097-0.01670.4412-0.00470.13280.01150.03950.27760.04120.414227.5767-35.453728.3871
124.3451.17410.52991.50880.44461.8340.04140.09770.0144-0.0987-0.2362-0.50550.16160.3820.10530.17710.03860.0330.2040.03830.320627.0387-41.239427.9325
138.5474-6.46636.02885.4834-6.22088.33070.32850.2782-0.2438-0.6429-0.2880.06680.82030.1141-0.03980.18110.00460.05110.1716-0.01060.178615.2924-46.980725.4137
140.5508-0.56520.31962.6416-0.43081.0012-0.0328-0.05140.04560.09670.0041-0.1161-0.02860.04920.00850.0864-0.00860.03250.14350.0070.13259.7581-32.727534.2476
154.8481-5.26414.78876.5606-5.04864.71030.0022-0.0788-0.1137-0.10550.09770.1404-0.0129-0.0977-0.04010.1441-0.02190.02080.1458-0.0090.1792-0.7911-20.901526.3779
161.28720.12460.17472.46830.27781.78710.04630.0267-0.0232-0.1439-0.0480.13180.1163-0.16790.01150.12480.00410.01660.17080.02570.18195.4711-36.858527.8913
175.14930.97595.35545.14581.27685.7286-0.4174-0.45880.2658-0.0438-0.217-0.5915-0.73410.0310.66910.1987-0.0219-0.0240.27810.06310.44623.6515-16.972829.4777
182.0865-0.0944-0.91111.7335-0.11854.580.04190.12850.0730.3361-0.03920.0753-0.50830.1167-0.05720.22170.01830.01270.139-0.0160.14375.0231-37.842656.6793
195.59541.4254-0.68536.8981-1.93688.4289-0.2573-0.0941-0.01660.16040.1028-1.02610.12760.85630.13920.19020.057-0.04370.226-0.05590.288817.5315-37.966862.9631
201.97880.03840.47992.4364-0.76765.21660.0089-0.1132-0.13430.36960.2681-0.17880.48630.3128-0.28010.32280.0778-0.02050.1654-0.03070.196612.2247-47.336461.6065
212.81370.7285-0.64683.6435-0.09333.9908-0.0185-0.2246-0.37580.3340.2806-0.34240.47730.5497-0.2690.32320.1061-0.00950.2308-0.06060.189910.982-48.992462.3696
224.8269-1.89090.47953.0623-4.87479.4137-0.14890.0708-0.40230.1760.04110.80590.2256-0.10570.0960.1965-0.01420.06120.1529-0.01960.2-2.3311-48.075461.7127
231.27960.6304-0.23871.69441.03982.0083-0.0401-0.2013-0.11540.62120.00940.09620.37850.02920.00070.38380.06360.04350.16530.03230.18172.5702-40.080773.7374
241.0011-1.16541.74895.7231-5.40015.654-0.32360.05320.21560.49170.27820.3594-0.4351-0.18680.0430.364-0.01010.02040.21320.0110.332-3.8039-19.577664.9229
254.9732.5711.19365.3711-0.32825.17180.065-0.1015-0.13040.6153-0.1590.85910.4466-0.36920.11030.33530.01010.15120.16660.00110.3617-9.2279-42.906167.6596
269.09564.27865.98624.41513.67246.7769-0.22531.40031.1478-0.15450.04820.9979-0.12590.31380.17580.33390.0431-0.00430.39770.1090.4822-11.3482-35.228160.426
276.50022.5587-1.5455.09970.85441.4725-0.0459-0.0530.18950.23750.08580.2809-0.0271-0.0334-0.0510.3160.0490.00130.12250.06460.19121.4362-29.782669.9709
282.7173-1.87661.09817.0565-3.12767.0679-0.8411-0.29180.9239-0.0018-0.1291-1.9731-0.27230.61280.96490.34170.0264-0.09130.31790.02560.650118.9044-25.359564.4558
291.61530.49370.44371.9715-0.4153.48740.0354-0.0448-0.15520.16070.0076-0.1886-0.05950.0141-0.03010.2784-0.0105-0.03160.1284-0.00190.154813.0148-2.627769.3943
302.82480.5280.14231.82250.30973.1066-0.07960.11580.1940.03510.1053-0.1349-0.42080.0144-0.02920.3672-0.0402-0.04420.13560.01550.207514.21167.198267.821
315.59913.4903-0.51347.9598-3.8297.1359-0.3304-0.30120.34590.530.19870.2345-0.7706-0.67790.13780.46960.1112-0.0390.2602-0.06580.18450.52089.474266.5059
322.4102-0.69121.14151.79520.72263.3680.00620.01080.0496-0.01450.0364-0.0032-0.1962-0.1913-0.06370.2531-0.03070.0040.14370.01210.1445.22890.620154.9178
331.44630.904-2.41323.851-5.39538.1933-0.12590.0602-0.25520.30160.04920.260.22990.08490.14530.2832-0.0037-0.01160.1629-0.00380.2801-2.1857-17.372362.5623
343.96494.9993-2.15928.8986-3.31573.2657-0.35110.36330.0081-0.20520.55890.64480.2957-0.1729-0.17330.25040.05920.00370.16890.02320.3101-4.6446-20.651564.1674
352.2701-0.56651.57943.0427-0.24563.0418-0.1765-0.4844-0.17260.50830.1730.56380.0269-0.6628-0.01240.30040.0050.05910.28040.02940.2201-4.0508-2.771261.8093
365.13114.5424-4.78886.9663-4.16914.5867-0.6260.4383-1.01520.17680.1677-0.99990.55610.18780.55730.3607-0.0232-0.03170.2943-0.04320.458119.2887-15.798965.1708
376.8458-2.54043.26757.0504-3.5487.6309-0.095-0.3549-0.35670.32230.1058-0.10530.19050.2427-0.01970.3227-0.0133-0.04410.1809-0.0410.191918.7793-2.733104.8646
386.4775-1.81531.37318.6739-5.04093.2435-0.0269-0.0853-0.39670.39010.072-0.49710.05730.6662-0.10460.28590.0149-0.08980.2384-0.04850.289825.0807-10.8394102.5411
394.6871-0.22170.79094.23080.75762.4587-0.13650.02110.14910.22050.0238-0.3239-0.22010.38870.12280.3012-0.0606-0.07660.1930.00570.234825.0946-0.1005103.8063
407.27751.3521-3.70324.45160.48047.08730.0782-0.13090.25760.17730.0937-0.507-0.7390.6084-0.18330.305-0.0424-0.13410.25150.04260.202224.77991.3158103.1089
419.24036.3436-5.36866.5371-5.07296.9345-0.0145-0.41280.93040.5024-0.08850.5107-0.83590.15320.08090.51590.0487-0.12460.2225-0.06350.289912.92827.0114104.4488
421.738-0.09520.37094.6101-0.09931.467-0.14420.03870.316-0.13310.0702-0.0133-0.51220.16420.05080.3399-0.0387-0.07460.1621-0.00270.192714.2272-0.588996.2783
434.8955-3.1426-0.13167.741-0.29651.0446-0.12560.23020.1339-0.231-0.00370.0158-0.18830.0050.18050.2731-0.0452-0.01960.23450.01770.140210.5271-3.709587.1517
440.36980.47660.23941.6317-1.4322.76120.1774-0.03650.14630.7501-0.04010.8095-0.1758-0.138-0.11810.30680.01090.11810.1764-0.01080.2766-0.5057-15.8186100.1353
457.47384.0635-4.3854.9791-3.38255.23910.02160.33650.51190.39440.28211.10590.098-0.4192-0.19230.27740.00380.07170.14950.02790.3639-3.876-17.9284101.5857
465.2596-1.3518-3.32473.99642.8474.577-0.3335-0.48090.51091.00510.3980.2261-0.8957-0.1675-0.07170.54280.1167-0.04060.22940.00240.26384.076.053898.8639
473.5954-1.35110.72943.9181-0.80362.7022-0.1909-0.31320.22670.65690.20980.397-0.3994-0.3959-0.0410.31270.02310.03630.21010.0180.22732.9375-5.5443100.9994
483.90634.0806-3.63116.813-4.85053.9291-0.02010.3191-0.907-0.1142-0.4065-0.99640.32060.17480.42430.27080.03550.00650.30780.01320.395519.8488-22.8321102.217
491.72990.0037-0.86393.08070.09894.54980.03250.0531-0.0144-0.20920.0271-0.3139-0.09460.1313-0.02740.1887-0.01890.0080.1267-0.0280.19793.7977-39.781796.9774
501.82790.3028-0.04872.37750.95747.2771-0.0137-0.0434-0.24380.15820.0929-0.07860.3517-0.0386-0.08610.2163-0.0204-0.01020.12520.00320.22120.2827-49.161398.6523
517.86492.7205-2.20063.5204-5.60369.77280.04650.2502-0.14230.1208-0.19490.34010.3116-0.77260.14110.2861-0.01410.02750.3242-0.08360.2348-12.7002-44.9745100.4584
526.69910.9748-3.24481.6883-0.98424.13730.1636-0.2612-0.25710.3815-0.1219-0.027-0.1457-0.0698-0.05920.2628-0.00550.00690.10880.0090.1623-4.1011-38.2011111.592
530.37592.3748-0.9268.1655-4.72772.69170.00520.12550.11310.36440.12130.3735-0.1531-0.2321-0.14030.20930.03730.04780.2225-0.0010.2372-2.5961-17.145102.9108
547.23690.01093.7318.9865-2.93965.98850.1890.3421-0.4537-0.22940.04320.7853-0.0759-0.7394-0.23130.22240.04470.04160.3543-0.03870.2483-16.8409-37.0488106.1488
557.4427-1.54626.17678.7517-3.80697.06580.1241.83530.8424-0.9454-0.08030.5673-0.5002-0.127-0.13330.44270.1025-0.02020.70650.11540.419-16.0077-29.316998.4982
566.31660.4676-2.75973.36380.32622.88070.16480.08080.2520.15670.02420.2399-0.348-0.1832-0.17840.25420.00980.02490.12260.02670.2055-1.835-28.5861107.4138
575.0003-6.42384.61929.6479-6.04314.422-0.5215-0.1499-0.01810.383-0.0014-1.1834-0.19140.13740.4370.27650.0054-0.00350.28640.01640.440615.9669-31.527100.7252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 83 )A42 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 98 )A84 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 132 )A99 - 132
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 169 )A133 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 183 )A170 - 183
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 201 )A184 - 201
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 220 )A202 - 220
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 234 )A221 - 234
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 21 )B1 - 21
11X-RAY DIFFRACTION11chain 'B' and (resid 22 through 67 )B22 - 67
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 83 )B68 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 99 )B84 - 99
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 150 )B100 - 150
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 169 )B151 - 169
16X-RAY DIFFRACTION16chain 'B' and (resid 170 through 220 )B170 - 220
17X-RAY DIFFRACTION17chain 'B' and (resid 221 through 236 )B221 - 236
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 21 )C1 - 21
19X-RAY DIFFRACTION19chain 'C' and (resid 22 through 41 )C22 - 41
20X-RAY DIFFRACTION20chain 'C' and (resid 42 through 67 )C42 - 67
21X-RAY DIFFRACTION21chain 'C' and (resid 68 through 83 )C68 - 83
22X-RAY DIFFRACTION22chain 'C' and (resid 84 through 98 )C84 - 98
23X-RAY DIFFRACTION23chain 'C' and (resid 99 through 132 )C99 - 132
24X-RAY DIFFRACTION24chain 'C' and (resid 133 through 169 )C133 - 169
25X-RAY DIFFRACTION25chain 'C' and (resid 170 through 183 )C170 - 183
26X-RAY DIFFRACTION26chain 'C' and (resid 184 through 201 )C184 - 201
27X-RAY DIFFRACTION27chain 'C' and (resid 202 through 220 )C202 - 220
28X-RAY DIFFRACTION28chain 'C' and (resid 221 through 236 )C221 - 236
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 41 )D1 - 41
30X-RAY DIFFRACTION30chain 'D' and (resid 42 through 83 )D42 - 83
31X-RAY DIFFRACTION31chain 'D' and (resid 84 through 98 )D84 - 98
32X-RAY DIFFRACTION32chain 'D' and (resid 99 through 132 )D99 - 132
33X-RAY DIFFRACTION33chain 'D' and (resid 133 through 150 )D133 - 150
34X-RAY DIFFRACTION34chain 'D' and (resid 151 through 169 )D151 - 169
35X-RAY DIFFRACTION35chain 'D' and (resid 170 through 220 )D170 - 220
36X-RAY DIFFRACTION36chain 'D' and (resid 221 through 236 )D221 - 236
37X-RAY DIFFRACTION37chain 'E' and (resid 1 through 21 )E1 - 21
38X-RAY DIFFRACTION38chain 'E' and (resid 22 through 41 )E22 - 41
39X-RAY DIFFRACTION39chain 'E' and (resid 42 through 67 )E42 - 67
40X-RAY DIFFRACTION40chain 'E' and (resid 68 through 83 )E68 - 83
41X-RAY DIFFRACTION41chain 'E' and (resid 84 through 98 )E84 - 98
42X-RAY DIFFRACTION42chain 'E' and (resid 99 through 118 )E99 - 118
43X-RAY DIFFRACTION43chain 'E' and (resid 119 through 132 )E119 - 132
44X-RAY DIFFRACTION44chain 'E' and (resid 133 through 150 )E133 - 150
45X-RAY DIFFRACTION45chain 'E' and (resid 151 through 169 )E151 - 169
46X-RAY DIFFRACTION46chain 'E' and (resid 170 through 183 )E170 - 183
47X-RAY DIFFRACTION47chain 'E' and (resid 184 through 220 )E184 - 220
48X-RAY DIFFRACTION48chain 'E' and (resid 221 through 236 )E221 - 236
49X-RAY DIFFRACTION49chain 'F' and (resid 1 through 41 )F1 - 41
50X-RAY DIFFRACTION50chain 'F' and (resid 42 through 83 )F42 - 83
51X-RAY DIFFRACTION51chain 'F' and (resid 84 through 99 )F84 - 99
52X-RAY DIFFRACTION52chain 'F' and (resid 100 through 132 )F100 - 132
53X-RAY DIFFRACTION53chain 'F' and (resid 133 through 169 )F133 - 169
54X-RAY DIFFRACTION54chain 'F' and (resid 170 through 183 )F170 - 183
55X-RAY DIFFRACTION55chain 'F' and (resid 184 through 201 )F184 - 201
56X-RAY DIFFRACTION56chain 'F' and (resid 202 through 220 )F202 - 220
57X-RAY DIFFRACTION57chain 'F' and (resid 221 through 236 )F221 - 236

+
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