[English] 日本語
Yorodumi
- PDB-9dr5: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dr5
TitleCrystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound, P1 form)
ComponentsCatechol 1,2-dioxygenase
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Catechol 1 / 2-dioxygenase
Function / homology
Function and homology information


catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase, proteobacteria / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / : / Intradiol ring-cleavage dioxygenases signature. / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia multivorans ATCC 17616 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound, P1 form)
Authors: Enayati, P. / Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catechol 1,2-dioxygenase
B: Catechol 1,2-dioxygenase
C: Catechol 1,2-dioxygenase
D: Catechol 1,2-dioxygenase
E: Catechol 1,2-dioxygenase
F: Catechol 1,2-dioxygenase
G: Catechol 1,2-dioxygenase
H: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,95858
Polymers276,1498
Non-polymers8,80950
Water45,3982520
1
A: Catechol 1,2-dioxygenase
B: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,18614
Polymers69,0372
Non-polymers2,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-130 kcal/mol
Surface area25530 Å2
MethodPISA
2
C: Catechol 1,2-dioxygenase
D: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,18614
Polymers69,0372
Non-polymers2,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-122 kcal/mol
Surface area25460 Å2
MethodPISA
3
E: Catechol 1,2-dioxygenase
F: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,29315
Polymers69,0372
Non-polymers2,25513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-117 kcal/mol
Surface area25880 Å2
MethodPISA
4
G: Catechol 1,2-dioxygenase
H: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,29315
Polymers69,0372
Non-polymers2,25513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-125 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.970, 86.270, 110.161
Angle α, β, γ (deg.)106.04, 96.74, 113.15
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Catechol 1,2-dioxygenase / BumuA.00117.a.B1


Mass: 34518.656 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans ATCC 17616 (bacteria)
Gene: catA / Plasmid: BumuA.00117.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KXJ8, catechol 1,2-dioxygenase

-
Non-polymers , 7 types, 2570 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2520 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20% 3350, 0.5M NaCl, 0.1M NaAc 4.6, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate 14238 well B2 drop 2. Protein was prepared in the presence if ZnCl2. Puck: PSL-1607, Cryo: 20% (v/v) PEG 200 ...Details: 20% 3350, 0.5M NaCl, 0.1M NaAc 4.6, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate 14238 well B2 drop 2. Protein was prepared in the presence if ZnCl2. Puck: PSL-1607, Cryo: 20% (v/v) PEG 200 + 80% (v/v) crystallant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 14, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.71→102.35 Å / Num. obs: 278593 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.041 / Rrim(I) all: 0.078 / Χ2: 1.02 / Net I/σ(I): 10.1 / Num. measured all: 987993
Reflection shellResolution: 1.71→1.75 Å / % possible obs: 95.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.709 / Num. measured all: 72882 / Num. unique obs: 20527 / CC1/2: 0.632 / Rpim(I) all: 0.439 / Rrim(I) all: 0.836 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→51.99 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 14078 5.05 %
Rwork0.1506 --
obs0.1522 278542 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18792 0 566 2520 21878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720229
X-RAY DIFFRACTIONf_angle_d0.86227328
X-RAY DIFFRACTIONf_dihedral_angle_d13.4497472
X-RAY DIFFRACTIONf_chiral_restr0.0532924
X-RAY DIFFRACTIONf_plane_restr0.0093646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.31084840.26788714X-RAY DIFFRACTION96
1.73-1.750.29634600.24948836X-RAY DIFFRACTION96
1.75-1.770.2724620.23968750X-RAY DIFFRACTION96
1.77-1.790.26094710.22858778X-RAY DIFFRACTION96
1.79-1.820.26764910.21548696X-RAY DIFFRACTION96
1.82-1.840.24875010.2068756X-RAY DIFFRACTION96
1.84-1.870.22134870.1878745X-RAY DIFFRACTION96
1.87-1.90.21944870.17658707X-RAY DIFFRACTION95
1.9-1.930.20914660.17068721X-RAY DIFFRACTION95
1.93-1.960.22324700.17368728X-RAY DIFFRACTION96
1.96-1.990.21095130.17278800X-RAY DIFFRACTION97
1.99-2.030.21914940.17998809X-RAY DIFFRACTION97
2.03-2.070.18864510.14618871X-RAY DIFFRACTION97
2.07-2.110.17244370.14038893X-RAY DIFFRACTION97
2.11-2.150.18844610.14068915X-RAY DIFFRACTION97
2.15-2.20.18954480.14128872X-RAY DIFFRACTION97
2.2-2.260.18044950.14038881X-RAY DIFFRACTION97
2.26-2.320.16334620.13138853X-RAY DIFFRACTION97
2.32-2.390.17574740.13338924X-RAY DIFFRACTION97
2.39-2.470.1734710.13558877X-RAY DIFFRACTION97
2.47-2.550.18144540.14268969X-RAY DIFFRACTION98
2.55-2.660.17594520.14568913X-RAY DIFFRACTION97
2.66-2.780.15864350.13788916X-RAY DIFFRACTION97
2.78-2.920.1784650.14618809X-RAY DIFFRACTION96
2.92-3.110.19455120.15838652X-RAY DIFFRACTION95
3.11-3.350.19634200.15728582X-RAY DIFFRACTION93
3.35-3.680.17314400.15158556X-RAY DIFFRACTION93
3.68-4.220.1614940.12478903X-RAY DIFFRACTION98
4.22-5.310.13675110.11949010X-RAY DIFFRACTION99
5.31-51.990.17944100.16229028X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.15580.05330.08940.1842-0.09810.1485-0.00060.04970.3431-0.0851-0.0039-0.0671-0.28580.259-0.00580.2666-0.0323-0.03450.21860.03880.3142-9.202763.4772-27.8475
20.6222-0.43060.42090.3944-0.24460.2954-0.03970.03370.09370.0175-0.0393-0.0558-0.02510.0575-00.1735-0.0190.00370.19690.02130.183-1.272648.9385-18.8081
30.1444-0.09260.11730.0837-0.0230.1424-0.1163-0.1929-0.03130.1108-0.0015-0.0411-0.07460.1198-0.00020.2127-0.0154-0.01610.2590.00570.20429.741243.47510.6043
40.6169-0.3162-0.06950.7779-0.15860.4056-0.0708-0.2623-0.10380.20050.05720.01590.0196-0.0072-0.00030.22760.00770.02360.26440.02950.18398.165532.24246.7806
50.6802-0.17930.22370.5697-0.22440.3697-0.0527-0.0035-0.03770.11390.0052-0.04870.03870.133-00.18930.00730.00630.22120.01160.184312.689233.1189-3.2299
60.3790.02520.17910.1758-0.0130.4329-0.1667-0.18850.13910.26740.0441-0.1018-0.1993-0.008-0.00190.24160.0039-0.02450.2502-0.00550.25310.658445.14084.554
70.2429-0.123-0.09860.2075-0.06520.1298-0.06990.17250.0572-0.26350.0254-0.1163-0.02610.2219-0.0140.1726-0.0151-0.00010.27550.00950.269211.903844.4376-22.7249
80.3265-0.12660.57840.1755-0.29790.7771-0.07570.03530.0945-0.0185-0.0041-0.0484-0.02210.0534-00.1668-0.01170.00910.17980.01580.1888-6.019550.3229-22.9999
90.7328-0.1398-0.19020.64310.27090.48660.01950.07140.0031-0.1042-0.04440.11740.0029-0.119200.1874-0.027-0.02540.204-0.00560.1907-35.493148.2086-29.8169
100.6652-0.1819-0.2390.5108-0.05330.4258-0.07840.11840.1808-0.08180.01190.0812-0.0549-0.0046-00.1932-0.0177-0.02650.17880.00620.2313-30.559456.9702-28.6786
110.30350.04680.31740.3324-0.00820.32940.06230.1796-0.114-0.2555-0.04870.09490.12620.014200.29710.0027-0.00460.25550.00410.2112-27.634546.2182-38.0267
120.2834-0.2272-0.14530.21550.00130.53340.1576-0.20080.21890.07930.0913-0.4-0.15980.56430.01580.2588-0.0431-0.01930.22020.00840.3025-27.778143.971-74.5311
130.3747-0.25740.29530.2189-0.27020.3316-0.03120.01980.050.0008-0.0745-0.11370.01110.081-0.00510.1678-0.0062-0.0150.19790.02390.2229-20.08228.5798-67.4054
140.3364-0.06970.26430.13820.05840.2902-0.0553-0.1223-0.01090.19360.0422-0.04080.0755-0.038300.24570.00250.00260.24190.03180.2407-10.825911.9973-44.4974
150.2534-0.2618-0.24880.25860.26220.3410.0437-0.1485-0.04920.1856-0.0357-0.02770.1245-0.0475-00.218-0.0039-0.00080.22120.02390.2013-10.456610.4952-44.09
160.1294-0.1785-0.10270.40720.06710.10430.0142-0.0474-0.05630.1282-0.00730.02820.16390.072700.2639-0.005-0.02010.24220.03620.2434-10.14818.6398-46.1839
170.42180.10670.28460.8856-0.03450.2215-0.00870.0383-0.02640.0264-0.0789-0.12430.04370.071-0.00080.20230.02820.00520.22720.04030.2389-6.300710.4989-53.8398
180.31320.1837-0.16020.20970.06780.5401-0.0583-0.21090.09720.19870.0267-0.091-0.0679-0.006300.23380.0049-0.04080.26740.0060.3203-8.162521.4793-44.7542
190.0342-0.08140.02111.0016-0.63510.4215-0.12470.28880.109-0.5592-0.0581-0.2727-0.02040.4675-0.07580.24010.01550.02510.30840.06930.343-6.992124.268-71.8013
200.3155-0.2140.46160.2346-0.40180.6584-0.04590.03750.11190.0046-0.0348-0.0961-0.00440.0773-00.1553-0.0076-0.00390.16930.01550.2065-24.597830.2975-71.099
210.84670.17780.20820.37870.21150.5341-0.01760.01370.0056-0.016-0.00090.03540.0416-0.0857-00.1779-0.0153-0.00020.1903-0.01150.1711-52.100930.1418-76.3562
220.66660.0625-0.05290.6402-0.10060.6594-0.05890.07910.0819-0.04470.03950.0574-0.0967-0.1172-00.17580.0128-0.00590.19350.00010.1919-53.084538.6443-79.3247
230.42150.26090.23070.4345-0.00270.34850.04220.1699-0.1242-0.161-0.05160.02290.0582-0.0226-00.22490.00620.01230.2145-0.00810.1834-46.703227.8429-86.1711
240.2399-0.1576-0.16380.17170.03920.1671-0.073-0.2734-0.13640.08390.0169-0.02750.21880.0329-0.01120.28090.02260.02020.21510.05060.2359-30.06576.155111.8386
250.2471-0.2792-0.24640.45590.12620.3164-0.0162-0.079-0.02580.07450.03060.07680.02170.0196-00.19370.0004-0.00330.1760.0090.1959-36.562423.10847.8942
260.07860.11990.03940.15470.05460.01750.0731-0.13890.05320.1148-0.0455-0.0766-0.02770.108-00.2023-0.0053-0.01270.2133-0.02570.2112-36.091547.44117.5424
270.5452-0.15970.14420.65090.00810.26070.0183-0.04080.0886-0.04030.0104-0.013-0.09010.040500.1642-0.01830.00130.1555-0.02390.182-35.766856.386411.0138
280.2487-0.07090.0270.1435-0.04290.0424-0.0017-0.02050.0196-0.0667-0.02060.011-0.03430.007300.2037-0.0021-0.00930.1702-0.00310.1926-41.057545.65553.8922
290.5724-0.0238-0.31520.62740.15270.63820.0127-0.01110.03870.07940.01080.1215-0.0374-0.016300.17940.0061-0.01510.1779-0.00290.2064-46.254153.489612.6461
300.19080.0330.05690.17320.04290.0772-0.0464-0.1767-0.03480.27230.1236-0.29670.13690.3082-0.01880.28430.0517-0.05150.2569-0.00820.1906-31.271740.620523.3991
310.1378-0.1915-0.08920.34030.06240.09-0.0218-0.069-0.04870.0110.03810.35380.0473-0.3046-0.01780.19540.00220.03140.23270.01150.2741-50.463326.16479.4602
320.3416-0.3181-0.21770.56870.2260.3371-0.0571-0.0363-0.03050.07040.02350.0520.0641-0.0144-00.2047-0.00610.00150.16780.01290.2049-34.340318.62125.3451
330.6988-0.1109-0.16650.8106-0.11060.4803-0.12240.1219-0.0102-0.30620.0161-0.06020.07620.0493-0.19310.3129-0.01930.06680.19780.00870.1841-14.866.205-14.8443
341.00810.190.31520.5310.18111.144-0.120.169-0.0705-0.2656-0.013-0.07510.21620.0777-0.61690.338-0.03090.08230.2078-0.00240.2405-12.58895.9934-12.5884
350.84750.1513-0.07720.8835-0.01180.2468-0.14620.0242-0.0989-0.12970.0291-0.06650.09510.064-0.03260.2550.01750.04840.16440.0180.2148-15.19993.3762-4.511
360.3312-0.162-0.14280.3148-0.05810.42190.02030.2219-0.1053-0.3185-0.0855-0.07010.1297-0.088-0.02740.3385-0.03320.01420.2108-0.00990.2628-25.49163.5033-14.9466
370.1545-0.1572-0.05080.2905-0.05030.08640.1220.0128-0.26280.24060.0288-0.10410.1380.12420.00080.2466-0.0211-0.00170.20510.03110.2021-49.8127-17.6045-42.257
380.2242-0.3188-0.19060.59410.16350.1890.0316-0.0389-0.00260.1004-0.03390.06270.0033-0.022800.1985-0.00950.0170.2008-0.00760.1592-55.70940.0403-43.7536
390.0177-0.057-0.03240.16690.10180.05740.0553-0.0280.0150.1035-0.08450.0060.0173-0.007600.1948-0.01210.00160.2366-0.02550.1897-56.646219.7723-31.8022
400.3419-0.08020.20820.5124-0.0480.26350.0031-0.04230.0928-0.0078-0.0452-0.0473-0.05380.0731-00.1764-0.01890.00190.2071-0.01510.1844-55.209131.576-37.6215
410.1199-0.11460.00410.5139-0.12460.3678-0.0182-0.02470.03930.0845-0.06160.05030.0409-0.0526-00.1616-0.0023-0.0010.21-0.03820.175-64.067424.5468-38.9623
420.27840.17720.03970.37750.31230.3502-0.0629-0.07210.0150.14320.0529-0.01790.0886-0.0091-00.23160.01410.01340.2396-0.01790.1989-55.281521.9262-28.0255
430.1189-0.0771-0.03130.3386-0.16970.39630.1104-0.089-0.0263-0.02990.10180.44490.3653-0.50830.0490.2219-0.04310.02440.2637-0.0020.2397-69.77552.7578-41.6847
440.5315-0.3992-0.27970.58020.22990.40080.06620.057-0.0348-0.0578-0.05820.00440.0329-0.01970.00020.20630.0146-0.00640.1786-0.0040.156-40.3495-13.2791-60.9396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 311 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 95 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 206 )
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 280 )
11X-RAY DIFFRACTION11chain 'B' and (resid 281 through 311 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 27 )
13X-RAY DIFFRACTION13chain 'C' and (resid 28 through 95 )
14X-RAY DIFFRACTION14chain 'C' and (resid 96 through 132 )
15X-RAY DIFFRACTION15chain 'C' and (resid 133 through 177 )
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 206 )
17X-RAY DIFFRACTION17chain 'C' and (resid 207 through 280 )
18X-RAY DIFFRACTION18chain 'C' and (resid 281 through 311 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 27 )
20X-RAY DIFFRACTION20chain 'D' and (resid 28 through 95 )
21X-RAY DIFFRACTION21chain 'D' and (resid 96 through 230 )
22X-RAY DIFFRACTION22chain 'D' and (resid 231 through 280 )
23X-RAY DIFFRACTION23chain 'D' and (resid 281 through 311 )
24X-RAY DIFFRACTION24chain 'E' and (resid 2 through 27 )
25X-RAY DIFFRACTION25chain 'E' and (resid 28 through 94 )
26X-RAY DIFFRACTION26chain 'E' and (resid 95 through 118 )
27X-RAY DIFFRACTION27chain 'E' and (resid 119 through 188 )
28X-RAY DIFFRACTION28chain 'E' and (resid 189 through 230 )
29X-RAY DIFFRACTION29chain 'E' and (resid 231 through 290 )
30X-RAY DIFFRACTION30chain 'E' and (resid 291 through 309 )
31X-RAY DIFFRACTION31chain 'F' and (resid 2 through 27 )
32X-RAY DIFFRACTION32chain 'F' and (resid 28 through 95 )
33X-RAY DIFFRACTION33chain 'F' and (resid 96 through 177 )
34X-RAY DIFFRACTION34chain 'F' and (resid 178 through 206 )
35X-RAY DIFFRACTION35chain 'F' and (resid 207 through 280 )
36X-RAY DIFFRACTION36chain 'F' and (resid 281 through 311 )
37X-RAY DIFFRACTION37chain 'G' and (resid 2 through 27 )
38X-RAY DIFFRACTION38chain 'G' and (resid 28 through 95 )
39X-RAY DIFFRACTION39chain 'G' and (resid 96 through 115 )
40X-RAY DIFFRACTION40chain 'G' and (resid 116 through 206 )
41X-RAY DIFFRACTION41chain 'G' and (resid 207 through 280 )
42X-RAY DIFFRACTION42chain 'G' and (resid 281 through 311 )
43X-RAY DIFFRACTION43chain 'H' and (resid 2 through 27 )
44X-RAY DIFFRACTION44chain 'H' and (resid 28 through 310 )

+
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