[English] 日本語
Yorodumi
- PDB-7zcc: yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zcc
TitleyxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)
ComponentsUncharacterized protein YxbC
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / JMJC / JMJC DOMAIN / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / HYDROXYLATION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD
Function / homology
Function and homology information


JmjC domain-containing / JmjC domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Uncharacterized protein YxbC
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsChowdhury, R. / Schofield, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)
Authors: Chowdhury, R. / Schofield, C.J.
History
DepositionMar 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: Uncharacterized protein YxbC
B: Uncharacterized protein YxbC
C: Uncharacterized protein YxbC
D: Uncharacterized protein YxbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,44537
Polymers155,2944
Non-polymers3,15033
Water14,538807
1
A: Uncharacterized protein YxbC
B: Uncharacterized protein YxbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,08017
Polymers77,6472
Non-polymers1,43315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-114 kcal/mol
Surface area26400 Å2
2
C: Uncharacterized protein YxbC
D: Uncharacterized protein YxbC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,36420
Polymers77,6472
Non-polymers1,71718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-163 kcal/mol
Surface area26190 Å2
Unit cell
Length a, b, c (Å)109.733, 109.733, 192.191
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Uncharacterized protein YxbC


Mass: 38823.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yxbC, yxaQ, BSU39880, VE7D / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P46327

-
Non-polymers , 5 types, 840 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: For details, please contact chowdhury.rzaman@gmail.com

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 105884 / % possible obs: 93.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.99 / Rsym value: 0.065 / Χ2: 1.158 / Net I/σ(I): 20.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym valueΧ2% possible all
1.85-1.923.72.1106000.80.7831.09794.6
1.92-1.993.7103500.5381.24191.5
1.99-2.083.799130.3511.22988.2
2.08-2.193.9109560.2361.10897.2
2.19-2.333.9109230.1651.13396.9
2.33-2.513.9108580.1261.14696.3
2.51-2.763.9105380.0931.21393.1
2.76-3.164101350.0641.22689.4
3.16-3.994.1110590.0441.17797.1
3.99-504.1105520.0371.02990.7

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VRB

1vrb


Resolution: 1.848→47.647 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 5161 4.88 %
Rwork0.1654 100698 -
obs0.1671 105859 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.9 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 152.39 Å2 / Biso mean: 42.5509 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 1.848→47.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10169 0 311 807 11287
Biso mean--74.25 47.25 -
Num. residues----1301
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8481-1.86910.29421650.2727330093
1.8691-1.89110.30751680.2558340495
1.8911-1.91410.26971780.234332894
1.9141-1.93830.26811780.2261333293
1.9383-1.96390.22792050.2132327292
1.9639-1.99080.28151450.2204321189
1.9908-2.01920.24821420.2177287081
2.0192-2.04930.261860.1876305686
2.0493-2.08140.22291960.1881346398
2.0814-2.11550.20262000.1722347797
2.1155-2.1520.18771600.1616350697
2.152-2.19110.18681830.1714346297
2.1911-2.23320.20541790.1611348497
2.2332-2.27880.17992050.1625340497
2.2788-2.32840.22651600.162348797
2.3284-2.38250.19321620.166347497
2.3825-2.44210.18711530.1594348097
2.4421-2.50810.22421550.1703344895
2.5081-2.58190.22571750.1671337895
2.5819-2.66530.20211480.1663341194
2.6653-2.76050.20421980.1596321791
2.7605-2.8710.18351720.1613297283
2.871-3.00170.22381350.1623314187
3.0017-3.15990.20752180.169349798
3.1599-3.35780.2341700.159355198
3.3578-3.6170.17831520.1445354498
3.617-3.98080.14281690.1331348596
3.9808-4.55650.14581610.126343294
4.5565-5.73910.17991350.1471306383
5.7391-47.6470.23272080.2154354995
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)
10.1452-0.1974-0.43851.57260.66741.8239-0.2822-0.0477-0.3647-0.3990.207-0.29470.6666-0.02490.06870.412-0.04790.10070.24090.0420.342319.8609-37.967147.7138
23.7528-0.2023-0.76732.7698-0.15944.24530.1813-0.5384-1.00240.3495-0.375-0.73140.20290.41830.04890.4643-0.0963-0.00790.26970.1730.523231.3434-36.346250.8646
30.4775-0.35650.23691.7308-2.28866.84790.0761-0.3575-0.5970.2235-0.0322-0.07150.5760.60870.00770.20720.0497-0.01590.27190.07960.379445.3833-31.488741.5219
41.2756-0.4244-0.65242.6866-0.48640.45890.07210.09380.195-0.18520.02690.0458-0.3342-0.04890.00380.26870.0289-0.01050.21470.00720.187241.7828-10.265639.0207
51.36290.3154-0.16723.4896-1.10053.1478-0.2018-0.17450.11840.28530.1277-0.2542-0.33390.2358-0.05490.204-0.0076-0.02930.2284-0.01750.207644.9207-13.588739.6931
62.98322.090.4851.64490.5690.4789-0.06320.0016-0.45670.15850.0004-0.30250.20880.02520.07640.26810.05310.03290.2270.02420.312833.0746-33.329535.7674
71.18710.16810.73710.44260.09221.678-0.12150.3027-0.03530.05130.0826-0.0095-0.01650.28170.08720.1933-0.0016-0.02280.19040.02640.224131.2775-27.491637.6054
81.86021.1133-0.30052.26550.48590.31420.0812-0.4002-0.00820.2055-0.1321-0.1878-0.04960.02650.00010.2196-0.0145-0.02210.23990.06210.205830.8248-22.611845.5299
92.045-0.55641.11062.0724-0.56992.0664-0.1692-0.12720.66970.2305-0.19680.2599-0.5732-0.13580.25690.4315-0.03050.06130.3384-0.00350.501919.2942-12.884344.1662
103.42930.04740.08222.3132-0.4670.19690.2241-0.3227-0.06930.5638-0.2991-0.0565-0.35240.30230.05350.3576-0.09320.02590.26230.05620.189826.5893-26.031351.5592
112.35370.5928-0.02281.8230.26860.91230.0782-0.24670.05170.3693-0.1219-0.1057-0.21070.2740.03790.2576-0.0567-0.00630.23980.06210.180130.652-22.999845.9307
123.00370.7265-0.96640.6949-1.12513.2069-0.07960.51990.4368-0.15930.22590.2524-0.0675-0.2438-0.09580.1948-0.0294-0.03090.33090.07630.289413.3354-19.661114.2639
130.40510.11850.49052.98262.86442.9262-0.11160.95440.5278-0.8928-0.04830.4014-0.4846-0.6445-0.07240.27470.0423-0.06990.69480.33690.57395.315-13.31969.589
143.63821.86790.96253.26220.80940.9256-0.03910.52540.15410.00420.0676-0.02620.0523-0.0236-0.0620.2508-0.01610.01480.2550.02330.21526.6652-27.708124.381
150.36-0.177-0.03413.3070.0094-0.0511-0.1674-0.03840.18990.05230.30670.1235-0.2365-0.4718-0.17950.43840.07770.00420.41450.15380.307228.1321.2629-1.3128
161.89890.40950.93922.06811.88946.1581-0.10550.38650.4503-0.38610.1506-0.0723-0.66240.2217-0.12250.3296-0.01060.02720.24650.08670.253439.967-0.0465-0.4591
173.5757-0.983-0.82253.0417-1.27183.63860.1899-0.03620.25180.0421-0.0794-0.335-0.43920.4064-0.06820.205-0.08540.00260.2279-0.00750.246849.1633-4.936313.5727
180.4929-0.31810.2933.4648-1.86551.06860.27310.0341-0.6708-0.2692-0.33440.04110.9474-0.3222-0.22540.4045-0.0251-0.08560.25-0.02220.441947.1816-26.735713.049
192.1692-0.4919-0.1254.81850.91724.35120.0636-0.2168-0.63720.06380.1077-0.24040.56150.2415-0.1960.23440.0186-0.08130.26460.00430.311450.2166-23.114613.6526
202.51240.19680.14461.2689-0.29021.48250.0407-0.03870.13790.15760.03650.1964-0.2372-0.141-0.01480.244-0.02160.00830.22890.01260.190835.7829-5.300613.8434
211.26330.789-0.49411.0669-0.24812.2234-0.20940.12390.09980.08820.22960.05110.0789-0.1441-0.0380.1776-0.0292-0.01110.21270.02210.16235.219-10.648711.3312
222.45730.1863-1.05093.40120.17941.4660.03530.1930.027-0.09150.1243-0.03350.02080.0332-0.19430.1928-0.0315-0.03240.27220.0070.145138.4412-14.72173.8174
233.66571.3966-0.46971.5407-0.47371.2705-0.44490.5484-0.96-0.38270.21-0.25390.5701-0.21310.14470.3519-0.07860.00230.3338-0.06630.303229.0364-26.13780.9207
245.15771.89030.07974.94020.59322.77120.10340.66980.0601-0.4802-0.04080.023-0.1280.0846-0.01180.2458-0.0149-0.04110.32580.07470.12436.3216-11.2331-3.1992
253.72591.124-0.25272.0709-0.27671.804-0.07570.3334-0.0996-0.2510.1361-0.05640.04610.051-0.09080.2288-0.0315-0.01180.23540.02040.1738.401-14.52543.3403
262.98910.37480.05111.2627-0.75732.96420.03510.08320.00680.0770.04170.18480.0559-0.1811-0.09620.15540.00320.0180.24080.01920.30910.9506-21.681326.1911
273.78460.20210.01762.4322-2.09784.3984-0.08980.1915-0.1620.35440.48540.73730.0453-0.3421-0.25670.14750.00450.02350.29780.00740.33092.9383-30.206927.6579
284.0406-0.28351.15612.3957-0.72041.39320.1778-0.17730.20810.08260.09150.4335-0.0573-0.2387-0.16460.17250.02270.04730.26910.09680.243325.422-11.505921.5958
290.76420.32910.59281.9340.5792.1455-0.2970.16870.36580.42730.2797-0.533-0.7564-0.0543-0.03080.44020.0226-0.11410.24010.03390.360420.510538.496716.7625
304.42221.23041.19392.5941.03543.6720.15570.81540.6521-0.3044-0.3591-1.0611-0.260.37250.18880.420.0574-0.00710.21830.22670.618231.378436.203213.1353
310.70220.4735-0.94282.9163-3.54947.42040.03870.38050.6655-0.1308-0.2039-0.1318-0.66360.51030.06110.2254-0.04770.00820.29180.0750.36945.359931.504522.5205
320.92051.29840.21814.28960.20370.0590.06710.0262-0.16930.29360.0205-0.16880.41130.0529-0.10010.2707-0.0217-0.00960.2442-0.00050.202741.967710.098825.0881
331.52370.3582-0.48243.8132-1.28273.1195-0.08450.0249-0.1078-0.1530.0205-0.37250.36880.22310.10720.2076-0.0150.02440.271-0.00370.212244.91513.579924.3843
343.2411-1.9021-0.64861.14090.35380.5184-0.0635-0.02680.4247-0.04360.0299-0.1714-0.1540.06310.08850.253-0.0683-0.02240.22810.01490.305933.233833.294128.0576
351.32090.2693-0.62750.58790.15381.35990.0402-0.2630.1931-0.11040.0243-0.1672-0.09060.24410.08040.1935-0.0070.02080.18080.03170.197731.283527.486826.4546
362.3883-1.13190.4531.88730.63180.46310.18030.32980.0612-0.1491-0.1988-0.16020.04820.1538-0.00280.21780.01850.02670.25320.05090.172830.972322.216418.4548
371.6747-0.0351-1.50782.1675-0.59432.3763-0.20220.1602-0.8034-0.1789-0.17790.29710.6945-0.12860.25630.4360.0141-0.05480.3565-0.03010.560519.056112.703920.205
383.65270.0285-0.54751.9151-0.4690.37730.24580.45870.1531-0.5048-0.2233-0.01130.23870.2047-0.06620.35260.0906-0.03120.30250.07230.224726.586626.056312.4996
392.27140.08190.19592.22460.60130.95860.06550.2642-0.0694-0.4384-0.082-0.16690.11960.23620.02750.24810.04550.00920.2410.07590.179630.670322.976918.1613
403.3786-0.9271.00580.9114-0.5942.4992-0.1024-0.572-0.33770.17240.22430.17690.12-0.2909-0.08540.18190.01810.02690.33160.07220.256613.268319.706949.8052
411.9604-0.47940.26326.7936-0.35083.3378-0.2042-1.2736-0.88810.66340.12490.25430.4708-0.50230.01530.32820.01360.08120.77040.40510.65395.250913.344554.6746
422.2681-2.1478-0.93793.4580.76511.0504-0.0146-0.3068-0.0678-0.04260.0323-0.0544-0.0614-0.069-0.09420.21440.0105-0.01440.20270.03050.16226.52627.9239.7022
430.60480.34360.11752.2415-0.47220.1157-0.1706-0.0538-0.5294-0.13590.42720.3380.47-0.549-0.2490.4621-0.094-0.00720.41620.15150.343128.1848-0.859465.385
441.69830.34790.34841.61291.34345.9183-0.1311-0.4852-0.58280.36840.3236-0.00160.95780.3837-0.19320.32560.0327-0.03790.29580.11750.24139.66860.003263.9062
452.4170.39770.55235.3963-1.24620.86960.25830.0558-0.2639-0.1899-0.1571-0.3940.49820.3841-0.07210.18940.07080.00110.2433-0.00360.213649.14624.640150.6637
463.05460.02190.02312.50423.13214.19330.15440.08571.0351-0.3383-0.1231-0.0505-1.0501-0.1034-0.13240.39040.03070.08980.21960.01360.432247.058926.209151.1505
472.4360.6853-0.03844.50370.58444.11550.14180.13030.6743-0.0970.171-0.192-0.49640.3208-0.270.2224-0.01180.09940.24020.01050.34950.230723.110250.4035
482.6069-0.03880.28171.2485-0.13971.19240.07920.0694-0.1763-0.09370.02130.19410.1612-0.0946-0.03720.22630.0255-0.00370.2160.00410.199635.76015.22150.2255
492.3671-0.51331.16011.3198-0.26432.27970.016-0.2931-0.085-0.04420.05920.03190.0458-0.2576-0.04790.18360.02020.02180.22660.01060.172635.228510.661452.7407
502.05630.1821.2553.03490.06911.6739-0.0083-0.23490.0805-0.02530.1758-0.09930.00760.0563-0.19190.17960.03150.0340.2501-0.0030.146738.666515.136160.2774
513.0558-1.14770.81171.9303-0.42511.2738-0.4756-0.55360.84080.46540.202-0.1503-0.5133-0.21370.17340.34740.0888-0.00960.366-0.07040.331429.192126.360963.2754
524.0585-1.4190.26973.2136-0.24141.74040.1207-0.4991-0.18840.4298-0.0785-0.0730.05470.1134-0.00390.2820.01460.02270.34130.08450.176836.311411.246267.2855
533.0247-0.7693-0.16841.6925-0.49531.2405-0.0378-0.24410.06060.25520.1093-0.0171-0.06260.1463-0.06110.21080.04450.00860.23930.01980.185238.420714.511260.7131
542.64430.21790.58561.5032-0.9772.8444-0.0473-0.1185-0.0982-0.1070.1410.137-0.0513-0.1946-0.190.18390.0274-0.00230.27420.02540.306210.945521.67837.8741
553.6390.8523-1.10523.0933-4.03945.4918-0.174-0.18420.18450.04520.55850.5528-0.1596-0.3985-0.2470.15-0.0151-0.03350.3489-0.00220.35552.849629.981436.3795
569.26090.6161-1.93091.8912-0.55092.06640.06440.1537-0.3313-0.16390.10330.38250.1377-0.2485-0.13210.1765-0.0126-0.04110.23840.08770.220726.033711.816642.3313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:28)A6 - 28
2X-RAY DIFFRACTION2(chain A and resid 29:44)A29 - 44
3X-RAY DIFFRACTION3(chain A and resid 45:60)A45 - 60
4X-RAY DIFFRACTION4(chain A and resid 61:75)A61 - 75
5X-RAY DIFFRACTION5(chain A and resid 76:95)A76 - 95
6X-RAY DIFFRACTION6(chain A and resid 96:122)A96 - 122
7X-RAY DIFFRACTION7(chain A and resid 123:137)A123 - 137
8X-RAY DIFFRACTION8(chain A and resid 138:158)A138 - 158
9X-RAY DIFFRACTION9(chain A and resid 159:204)A159 - 204
10X-RAY DIFFRACTION10(chain A and resid 205:221)A205 - 221
11X-RAY DIFFRACTION11(chain A and resid 222:242)A222 - 242
12X-RAY DIFFRACTION12(chain A and resid 243:271)A243 - 271
13X-RAY DIFFRACTION13(chain A and resid 272:298)A272 - 298
14X-RAY DIFFRACTION14(chain A and resid 299:328)A299 - 328
15X-RAY DIFFRACTION15(chain B and resid 4:28)B4 - 28
16X-RAY DIFFRACTION16(chain B and resid 29:44)B29 - 44
17X-RAY DIFFRACTION17(chain B and resid 45:60)B45 - 60
18X-RAY DIFFRACTION18(chain B and resid 61:75)B61 - 75
19X-RAY DIFFRACTION19(chain B and resid 76:95)B76 - 95
20X-RAY DIFFRACTION20(chain B and resid 96:122)B96 - 122
21X-RAY DIFFRACTION21(chain B and resid 123:137)B123 - 137
22X-RAY DIFFRACTION22(chain B and resid 138:158)B138 - 158
23X-RAY DIFFRACTION23(chain B and resid 159:204)B159 - 204
24X-RAY DIFFRACTION24(chain B and resid 205:221)B205 - 221
25X-RAY DIFFRACTION25(chain B and resid 222:242)B222 - 242
26X-RAY DIFFRACTION26(chain B and resid 243:271)B243 - 271
27X-RAY DIFFRACTION27(chain B and resid 272:298)B272 - 298
28X-RAY DIFFRACTION28(chain B and resid 299:328)B299 - 328
29X-RAY DIFFRACTION29(chain C and resid 5:28)C5 - 28
30X-RAY DIFFRACTION30(chain C and resid 29:44)C29 - 44
31X-RAY DIFFRACTION31(chain C and resid 45:60)C45 - 60
32X-RAY DIFFRACTION32(chain C and resid 61:75)C61 - 75
33X-RAY DIFFRACTION33(chain C and resid 76:95)C76 - 95
34X-RAY DIFFRACTION34(chain C and resid 96:122)C96 - 122
35X-RAY DIFFRACTION35(chain C and resid 123:137)C123 - 137
36X-RAY DIFFRACTION36(chain C and resid 138:158)C138 - 158
37X-RAY DIFFRACTION37(chain C and resid 159:204)C159 - 204
38X-RAY DIFFRACTION38(chain C and resid 205:221)C205 - 221
39X-RAY DIFFRACTION39(chain C and resid 222:242)C222 - 242
40X-RAY DIFFRACTION40(chain C and resid 243:271)C243 - 271
41X-RAY DIFFRACTION41(chain C and resid 272:298)C272 - 298
42X-RAY DIFFRACTION42(chain C and resid 299:328)C299 - 328
43X-RAY DIFFRACTION43(chain D and resid 5:28)D5 - 28
44X-RAY DIFFRACTION44(chain D and resid 29:44)D29 - 44
45X-RAY DIFFRACTION45(chain D and resid 45:60)D45 - 60
46X-RAY DIFFRACTION46(chain D and resid 61:75)D61 - 75
47X-RAY DIFFRACTION47(chain D and resid 76:95)D76 - 95
48X-RAY DIFFRACTION48(chain D and resid 96:122)D96 - 122
49X-RAY DIFFRACTION49(chain D and resid 123:137)D123 - 137
50X-RAY DIFFRACTION50(chain D and resid 138:158)D138 - 158
51X-RAY DIFFRACTION51(chain D and resid 159:204)D159 - 204
52X-RAY DIFFRACTION52(chain D and resid 205:221)D205 - 221
53X-RAY DIFFRACTION53(chain D and resid 222:242)D222 - 242
54X-RAY DIFFRACTION54(chain D and resid 243:271)D243 - 271
55X-RAY DIFFRACTION55(chain D and resid 272:298)D272 - 298
56X-RAY DIFFRACTION56(chain D and resid 299:328)D299 - 328

+
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