[English] 日本語
Yorodumi
- PDB-6xhs: Crystal structure of S. aureus TarI in complex with CTP (space gr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xhs
TitleCrystal structure of S. aureus TarI in complex with CTP (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
CYTIDINE-5'-TRIPHOSPHATE / THIOCYANATE ION / Ribitol-5-phosphate cytidylyltransferase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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)175,90011
Polymers174,7936
Non-polymers1,1075
Water18010
1
A: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7483
Polymers58,2642
Non-polymers4831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22 kcal/mol
Surface area19520 Å2
MethodPISA
2
C: Ribitol-5-phosphate cytidylyltransferase 1
D: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3233
Polymers58,2642
Non-polymers581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area20130 Å2
MethodPISA
3
E: Ribitol-5-phosphate cytidylyltransferase 1
F: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8305
Polymers58,2642
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-39 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.357, 138.521, 109.564
Angle α, β, γ (deg.)90.000, 96.460, 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 20...
21(chain B and (resid 1 or (resid 2 and (name...
31(chain C and (resid 1 through 11 or (resid 20...
41(chain D and (resid 1 or (resid 2 and (name...
51(chain E and (resid 1 through 11 or (resid 20...
61(chain F and (resid 1 through 11 or (resid 20...

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 20...AA1 - 111 - 11
12LEULEULEULEU(chain A and (resid 1 through 11 or (resid 20...AA2020
13METMETGLYGLY(chain A and (resid 1 through 11 or (resid 20...AA1 - 2341 - 234
14METMETGLYGLY(chain A and (resid 1 through 11 or (resid 20...AA1 - 2341 - 234
15METMETGLYGLY(chain A and (resid 1 through 11 or (resid 20...AA1 - 2341 - 234
16METMETGLYGLY(chain A and (resid 1 through 11 or (resid 20...AA1 - 2341 - 234
21METMETMETMET(chain B and (resid 1 or (resid 2 and (name...BB11
22LYSLYSLYSLYS(chain B and (resid 1 or (resid 2 and (name...BB22
23METMETILEILE(chain B and (resid 1 or (resid 2 and (name...BB1 - 2351 - 235
24METMETILEILE(chain B and (resid 1 or (resid 2 and (name...BB1 - 2351 - 235
25METMETILEILE(chain B and (resid 1 or (resid 2 and (name...BB1 - 2351 - 235
26METMETILEILE(chain B and (resid 1 or (resid 2 and (name...BB1 - 2351 - 235
31METMETILEILE(chain C and (resid 1 through 11 or (resid 20...CC1 - 111 - 11
32LEULEULEULEU(chain C and (resid 1 through 11 or (resid 20...CC2020
33METMETALAALA(chain C and (resid 1 through 11 or (resid 20...CC1 - 2361 - 236
34METMETALAALA(chain C and (resid 1 through 11 or (resid 20...CC1 - 2361 - 236
35METMETALAALA(chain C and (resid 1 through 11 or (resid 20...CC1 - 2361 - 236
41METMETMETMET(chain D and (resid 1 or (resid 2 and (name...DD11
42LYSLYSLYSLYS(chain D and (resid 1 or (resid 2 and (name...DD22
43METMETILEILE(chain D and (resid 1 or (resid 2 and (name...DD1 - 2351 - 235
44METMETILEILE(chain D and (resid 1 or (resid 2 and (name...DD1 - 2351 - 235
45METMETILEILE(chain D and (resid 1 or (resid 2 and (name...DD1 - 2351 - 235
46METMETILEILE(chain D and (resid 1 or (resid 2 and (name...DD1 - 2351 - 235
51METMETILEILE(chain E and (resid 1 through 11 or (resid 20...EE1 - 111 - 11
52LEULEULEULEU(chain E and (resid 1 through 11 or (resid 20...EE2020
53METMETARGARG(chain E and (resid 1 through 11 or (resid 20...EE1 - 2321 - 232
61METMETILEILE(chain F and (resid 1 through 11 or (resid 20...FF1 - 111 - 11
62LEULEULEULEU(chain F and (resid 1 through 11 or (resid 20...FF2020
63METMETILEILE(chain F and (resid 1 through 11 or (resid 20...FF1 - 2351 - 235

-
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-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.25 M sodium thiocyanate, 22.5% PEG3350, 20 mM CTP, 20 mM magnesium chloride

-
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: Feb 10, 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: 2.9→49.044 Å / Num. obs: 32332 / % possible obs: 99.65 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rpim(I) all: 0.1079 / Net I/σ(I): 6.08
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 3173 / CC1/2: 0.539 / Rpim(I) all: 0.5925 / % possible all: 99.81

-
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: 2.9→49.044 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2669 1617 5 %
Rwork0.2099 30694 -
obs0.2132 32311 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.21 Å2 / Biso mean: 60.94 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 2.9→49.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10463 0 94 10 10567
Biso mean--61.66 27.58 -
Num. residues----1394
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3906X-RAY DIFFRACTION6.085TORSIONAL
12B3906X-RAY DIFFRACTION6.085TORSIONAL
13C3906X-RAY DIFFRACTION6.085TORSIONAL
14D3906X-RAY DIFFRACTION6.085TORSIONAL
15E3906X-RAY DIFFRACTION6.085TORSIONAL
16F3906X-RAY DIFFRACTION6.085TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.98540.39631320.32572505100
2.9854-3.08170.35921360.31322570100
3.0817-3.19180.37781330.29792529100
3.1918-3.31960.3251350.27312575100
3.3196-3.47060.30221340.25572543100
3.4706-3.65360.30011350.23112565100
3.6536-3.88240.29141340.21282547100
3.8824-4.1820.22871360.18342571100
4.182-4.60260.23491340.159254599
4.6026-5.26790.20951340.15962555100
5.2679-6.63440.26271360.21282577100
6.6344-49.0440.2181380.173261299
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)
12.8441-2.12891.54583.2349-2.47868.778-0.3679-0.26560.54440.20880.1592-0.3871-0.06060.22720.16030.3041-0.00220.03370.2558-0.03140.45996.7913-0.285535.002
23.1433-0.6520.68152.7702-0.35153.6834-0.12120.04380.2611-0.0088-0.0189-0.0749-0.61470.08610.14970.3286-0.1148-0.00130.2834-0.01130.28532.62086.800827.5774
37.3859-4.3157-3.21493.9049-0.58536.19610.29320.8438-0.148-1.013-0.50320.1749-0.48491.23790.30530.7341-0.09150.01030.530.00460.31782.1764-2.287312.2275
40.7429-0.521-0.26655.82-1.77420.4136-0.1391-0.2932-0.3252-0.32970.1080.2579-0.07870.1244-0.00170.39780.00760.0040.3690.03610.3553-2.544-15.956624.1595
52.05182.4754-1.00029.4282.39822.4613-0.1086-0.55540.34860.6523-0.48540.99681.2444-0.50430.43770.4625-0.0759-0.03990.62150.09790.6648-13.7858-8.142630.6988
66.8383-0.86792.97754.16050.87731.953-0.20870.0747-0.268-0.26810.2476-0.1974-0.10760.1568-0.04160.4468-0.04650.03860.3230.10270.29156.1027-9.820924.8843
77.27571.1476-2.41668.4662-0.79234.24320.0389-0.3130.2888-0.3807-0.2512-0.8808-0.10080.56430.28260.22520.12860.11020.56920.01570.480524.2735-35.459930.3514
81.67361.1516-0.36164.22431.07472.2458-0.19921.0428-0.47580.07790.6394-1.0898-0.5588-0.223-0.44450.32110.08870.08340.7149-0.02150.876729.3461-40.289225.2054
90.9198-0.4621-0.5695.6583.03654.5673-0.0621-0.1549-0.08410.1623-0.0168-0.25310.4409-0.03490.07320.2711-0.01660.05920.3220.05730.360914.0765-40.542633.5987
102.9317-3.45333.54654.3393-5.5287.6468-0.26290.12090.2769-0.1972-0.0626-0.1337-0.46910.12780.33590.4063-0.0299-0.01950.35450.01370.40250.5965-22.06726.9364
112.4749-0.81232.02198.96263.23666.178-0.11960.7001-0.41880.13730.1241.6266-0.74960.01620.09050.4308-0.02390.18410.4386-0.01220.46126.0944-45.036229.833
128.12310.6879-5.99020.0885-0.84017.20470.00920.81060.8706-0.50380.04410.5758-0.3838-1.0306-0.18510.88190.0976-0.01810.44640.0920.3641.3164-39.37321.7855
135.03790.4289-1.06613.6524-2.46423.54660.07790.18230.98150.108-0.0839-0.16990.7176-0.04380.00270.05140.0641-0.02180.30950.02810.479714.8358-23.990831.4103
144.89821.3014-3.01565.5821.14947.2862-0.3542-0.2789-0.33420.30190.1808-0.41720.31710.38880.15730.3840.1186-0.01470.3017-0.04210.307810.5466-40.57962.3567
155.9121-1.0438-1.71165.71750.63386.6587-0.4833-0.0912-0.30130.77210.5254-0.20880.15-0.059-0.10440.44670.05320.01370.21150.010.26247.0211-48.378559.4597
160.8087-0.5309-0.7193.4221.69370.83560.0329-0.5312-0.17021.5020.20150.11480.3432-0.096-0.11770.70170.050.07460.45210.17230.41292.0617-40.230173.4074
173.1582-1.10041.89220.56690.50257.1542-0.5996-0.07420.50910.0246-0.1148-0.1316-0.37770.65120.55670.48380.03360.020.34120.05730.4767-2.6755-21.339966.018
185.896-0.4554-2.06668.3572-0.64596.0313-1.62290.1290.7016-0.06360.04210.61070.1338-0.69261.68320.73540.0469-0.30080.3277-0.10311.0111-7.648-13.619261.5488
196.91711.441.12917.99310.94774.55720.6269-0.1267-0.35991.19120.17620.91520.4226-0.3849-0.67830.34910.04410.13290.39410.19590.5814-5.5761-37.798968.0964
202.43321.3862.06055.5648-2.90655.90320.34392.09810.57860.14550.14440.3819-1.05990.2371-0.55150.5267-0.14910.00580.90870.04760.7265-12.0075-35.774860.1304
216.6985-0.33380.00474.8157-0.79243.713-0.3737-0.2970.50460.32590.42790.0472-0.6491-0.243-0.14390.57960.00810.01440.20930.02060.30991.5688-29.608269.8493
227.0006-2.2653-0.36444.858-5.40138.9906-0.9463-0.9110.832-1.0623-0.8282-1.29040.5711.69521.18170.47-0.02070.18780.5815-0.01220.779718.6988-25.428964.7548
234.0615-1.09721.66225.36810.0037.06690.107-0.00950.1286-0.0217-0.1498-0.3792-0.42460.32850.05180.4881-0.04840.0290.2989-0.0380.291812.6251-0.293467.3879
244.9837-0.6105-0.52131.5981.31734.4509-0.5854-0.50370.41370.55850.4061-0.0125-0.12590.19490.1770.8574-0.00470.03720.3582-0.0810.384915.15667.344271.4182
253.6255-1.51541.8985.2211-1.2824.4332-0.1167-0.13420.29630.4150.1369-0.1858-0.2461-0.65640.03130.7259-0.00610.05780.3553-0.00270.33273.80493.292958.7471
262.30122.7-3.72095.8506-5.2665.9196-0.1062-0.19080.03840.62510.01650.11880.04690.0890.09770.51830.00990.01780.3320.03370.4373-3.692-19.210563.2424
274.03772.2096-1.4825.9547-2.44022.0703-0.1515-0.19240.38290.84510.88351.1994-0.6519-1.2343-0.75710.70.14360.03920.65550.14840.6572-8.08951.590963.8438
284.42020.49792.28382.2638-1.91566.56930.091-0.4302-0.73470.28130.2640.20330.2748-0.3372-0.1890.54380.02270.01560.24250.06820.36092.9535-9.872658.7084
296.52831.8641-2.60335.6674-5.67586.4555-1.53490.5438-0.56020.11130.3052-1.27-0.3478-0.52631.20210.9313-0.04560.12730.3469-0.13510.662919.189-16.163365.9272
307.6673-1.93053.50594.42611.23612.6232-1.1676-0.0923-0.90370.53770.7384-0.5318-0.6918-0.86090.33810.4889-0.0430.09670.4971-0.12640.349517.7142-6.208108.5997
317.3711-2.67122.28249.2297-2.89079.6986-0.56380.2107-0.4050.95310.4662-0.6996-0.18970.56870.12060.49860.0737-0.12250.4373-0.13460.564524.6831-10.3953102.5851
324.5121-2.10921.06324.4626-2.11722.0812-0.23210.2554-0.05120.23850.1205-0.8782-1.29641.280.27730.6289-0.1922-0.04890.5080.00070.575325.0241-0.0684103.6211
334.8681-2.1475-0.74463.8828-1.13883.57150.2836-0.51260.2434-0.2666-0.64680.0626-0.95460.87330.28290.6127-0.1568-0.19220.62250.01730.475624.29342.0162103.1327
343.3384.0596-0.89855.913-0.72474.52730.2041-0.60440.95131.28450.08820.208-2.3197-0.6124-0.21081.02410.0682-0.24930.48060.00160.61312.57457.2597104.7715
355.65091.07331.85919.3468-2.0778.9294-0.82050.03460.70091.06920.5933-0.3157-1.5204-0.83040.22460.4469-0.0034-0.08680.5047-0.01880.311714.025-0.377896.4938
364.03751.628-3.79285.863-0.11238.10880.06710.16130.3989-1.62920.40110.3070.33080.1915-0.39360.6937-0.1273-0.11510.520.06360.450810.3292-3.498787.3821
373.99354.6249-3.65627.9003-4.50213.26380.1755-0.63160.38751.89020.03090.6605-0.90210.2989-0.34450.43280.00480.03980.5280.13790.4722-0.4529-15.60799.718
386.68820.57311.0110.33361.07354.24890.81671.38940.74211.31180.92951.78530.6304-0.7824-1.00861.00910.04740.20360.32920.42770.8675-3.8761-17.3289101.2656
397.9737-0.62531.3834.1162-4.10864.17480.43310.4070.55681.00130.34780.6784-1.3755-0.3043-0.17270.60770.0356-0.0690.62040.14060.60524.53466.094198.7065
408.3603-0.2967-4.50216.70751.71582.923-0.1998-3.58140.10291.70720.2170.41010.34010.4023-0.0251.32710.209-0.01331.83920.12120.7335-1.2240.7782108.4013
415.06151.74513.44683.8781-1.42748.1747-0.00880.13650.4999-0.17320.30451.5742-0.8332-0.8638-0.140.53460.1079-0.01120.61160.27340.6699-1.001-2.199595.6952
429.3775-5.50964.51445.6222-2.72359.59470.2904-0.1175-1.72750.6723-0.1125-0.177-0.17140.5663-0.21290.535-0.1007-0.11650.40180.09360.769616.3491-19.7646102.2698
433.9389-1.10970.02882.8050.37713.2862-0.1780.01880.05170.23190.131-0.3714-0.1834-0.12820.0640.6861-0.0043-0.03520.37240.01340.45462.2959-43.333197.3219
449.19452.66011.84446.07660.16871.543-0.20040.1072-0.3517-0.3350.17140.2570.3627-0.11050.08360.9728-0.0430.09440.4641-0.02330.4078-5.8751-44.5433102.5139
452.11081.14431.84333.6704-1.35522.70580.35520.155-0.09761.1312-0.33160.1599-0.2320.38980.06050.91160.05890.19090.50530.00720.4202-3.0645-22.9743107.0436
465.60532.03320.17076.5351.15364.01260.2598-0.3122-0.16670.50840.13890.447-0.2202-0.4238-0.33920.57680.04840.05690.40890.15030.4066-3.8596-31.4317103.7992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 118 )A32 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 132 )A119 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 182 )A133 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 195 )A183 - 195
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 234 )A196 - 234
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 54 )B1 - 54
8X-RAY DIFFRACTION8chain 'B' and (resid 55 through 83 )B55 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 132 )B84 - 132
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 169 )B133 - 169
11X-RAY DIFFRACTION11chain 'B' and (resid 170 through 182 )B170 - 182
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 201 )B183 - 201
13X-RAY DIFFRACTION13chain 'B' and (resid 202 through 235 )B202 - 235
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 54 )C1 - 54
15X-RAY DIFFRACTION15chain 'C' and (resid 55 through 98 )C55 - 98
16X-RAY DIFFRACTION16chain 'C' and (resid 99 through 132 )C99 - 132
17X-RAY DIFFRACTION17chain 'C' and (resid 133 through 150 )C133 - 150
18X-RAY DIFFRACTION18chain 'C' and (resid 151 through 163 )C151 - 163
19X-RAY DIFFRACTION19chain 'C' and (resid 164 through 182 )C164 - 182
20X-RAY DIFFRACTION20chain 'C' and (resid 183 through 201 )C183 - 201
21X-RAY DIFFRACTION21chain 'C' and (resid 202 through 220 )C202 - 220
22X-RAY DIFFRACTION22chain 'C' and (resid 221 through 236 )C221 - 236
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 54 )D1 - 54
24X-RAY DIFFRACTION24chain 'D' and (resid 55 through 83 )D55 - 83
25X-RAY DIFFRACTION25chain 'D' and (resid 84 through 132 )D84 - 132
26X-RAY DIFFRACTION26chain 'D' and (resid 133 through 169 )D133 - 169
27X-RAY DIFFRACTION27chain 'D' and (resid 170 through 201 )D170 - 201
28X-RAY DIFFRACTION28chain 'D' and (resid 202 through 220 )D202 - 220
29X-RAY DIFFRACTION29chain 'D' and (resid 221 through 235 )D221 - 235
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 21 )E1 - 21
31X-RAY DIFFRACTION31chain 'E' and (resid 22 through 41 )E22 - 41
32X-RAY DIFFRACTION32chain 'E' and (resid 42 through 67 )E42 - 67
33X-RAY DIFFRACTION33chain 'E' and (resid 68 through 83 )E68 - 83
34X-RAY DIFFRACTION34chain 'E' and (resid 84 through 98 )E84 - 98
35X-RAY DIFFRACTION35chain 'E' and (resid 99 through 118 )E99 - 118
36X-RAY DIFFRACTION36chain 'E' and (resid 119 through 132 )E119 - 132
37X-RAY DIFFRACTION37chain 'E' and (resid 133 through 150 )E133 - 150
38X-RAY DIFFRACTION38chain 'E' and (resid 151 through 169 )E151 - 169
39X-RAY DIFFRACTION39chain 'E' and (resid 170 through 182 )E170 - 182
40X-RAY DIFFRACTION40chain 'E' and (resid 183 through 195 )E183 - 195
41X-RAY DIFFRACTION41chain 'E' and (resid 196 through 210 )E196 - 210
42X-RAY DIFFRACTION42chain 'E' and (resid 211 through 232 )E211 - 232
43X-RAY DIFFRACTION43chain 'F' and (resid 1 through 67 )F1 - 67
44X-RAY DIFFRACTION44chain 'F' and (resid 68 through 118 )F68 - 118
45X-RAY DIFFRACTION45chain 'F' and (resid 119 through 169 )F119 - 169
46X-RAY DIFFRACTION46chain 'F' and (resid 170 through 235 )F170 - 235

+
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