[English] 日本語
Yorodumi
- PDB-8oro: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oro
TitleCRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER HYPEROXYC CONDITIONS
Components1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE COMPLEX / DIOXYGENASE / COFACTOR-DEVOID
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
OXYGEN MOLECULE / D(-)-TARTARIC ACID / 2-methyl-quinolin-4(1H)-one / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesPaenarthrobacter nitroguajacolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBui, S. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/I020411/1 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold.
Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A.
History
DepositionApr 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,64512
Polymers66,5472
Non-polymers1,09810
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-1 kcal/mol
Surface area22290 Å2
Unit cell
Length a, b, c (Å)120.110, 120.110, 44.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase


Mass: 33273.391 Da / Num. of mol.: 2 / Mutation: C69S, S101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria)
Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Production host: Escherichia coli (E. coli)
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase

-
Non-polymers , 6 types, 420 molecules

#2: Chemical ChemComp-VFH / 2-methyl-quinolin-4(1H)-one


Mass: 159.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.854
pseudo-merohedral22-K, -H, -L20.146
ReflectionResolution: 2→60.05 Å / Num. obs: 43233 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.093 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3144 / Rpim(I) all: 0.406 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→60.05 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.504 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2687 2154 4.984 %
Rwork0.2274 41062 -
all0.229 --
obs-43216 98.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.482 Å2
Baniso -1Baniso -2Baniso -3
1-3.426 Å20 Å20 Å2
2--3.426 Å20 Å2
3----6.852 Å2
Refinement stepCycle: LAST / Resolution: 2→60.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 75 410 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154275
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6416478
X-RAY DIFFRACTIONr_angle_other_deg1.1681.5879868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61821.557289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28115751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2561539
X-RAY DIFFRACTIONr_chiral_restr0.060.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021147
X-RAY DIFFRACTIONr_nbd_refined0.1840.21069
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.24207
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22205
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2377
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.225
X-RAY DIFFRACTIONr_nbd_other0.3030.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.29
X-RAY DIFFRACTIONr_mcbond_it0.3911.5882215
X-RAY DIFFRACTIONr_mcbond_other0.3911.5882216
X-RAY DIFFRACTIONr_mcangle_it0.6112.3792776
X-RAY DIFFRACTIONr_mcangle_other0.6112.3792775
X-RAY DIFFRACTIONr_scbond_it0.4011.6382539
X-RAY DIFFRACTIONr_scbond_other0.4011.6392540
X-RAY DIFFRACTIONr_scangle_it0.5952.4413695
X-RAY DIFFRACTIONr_scangle_other0.5952.4423696
X-RAY DIFFRACTIONr_lrange_it3.07230.67920842
X-RAY DIFFRACTIONr_lrange_other2.80630.27820550
X-RAY DIFFRACTIONr_ncsr_local_group_10.0580.059738
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.057830.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.057830.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3181520.2429710.24431830.9690.98398.1150.233
2.052-2.1080.2961550.22929520.23331170.9760.98599.67920.222
2.108-2.1690.2731470.2328380.23230190.9740.98398.87380.22
2.169-2.2350.3271390.22627390.23129600.9620.98197.22970.217
2.235-2.3080.2611450.21526910.21728480.9730.98399.57870.204
2.308-2.3890.2631320.21725990.21927520.9680.9899.23690.206
2.389-2.4790.2711340.23525410.23726780.9560.96999.8880.224
2.479-2.5790.2731240.22224360.22425710.9590.97299.57210.212
2.579-2.6930.271200.22523040.22724740.9570.9797.9790.212
2.693-2.8240.2441190.22422440.22523730.9590.96699.57860.212
2.824-2.9760.2631150.24221390.24322660.9450.9599.47040.233
2.976-3.1550.2621040.23220040.23421170.9360.95399.57490.224
3.155-3.370.2691000.23218950.23320100.9370.95199.25370.225
3.37-3.6380.296950.22417490.22818830.9120.95597.92880.22
3.638-3.9810.266850.21816330.22117370.9360.95398.90620.217
3.981-4.4430.238800.21514850.21715870.9430.95698.61370.215
4.443-5.1170.244680.22112980.22213960.9490.95497.8510.222
5.117-6.2340.262610.23911180.2412100.9580.95197.4380.244
6.234-8.6790.29500.258890.2529530.930.94398.53090.253
8.679-35.0050.268290.245370.2415770.9620.94898.09360.257
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)
112.0017-7.5257-4.321810.00294.32685.7267-0.3166-0.42870.15140.41280.3742-0.2420.15660.2146-0.05760.1844-0.0015-0.02230.15440.04890.1547-54.331325.988313.0757
22.10471.00422.514711.53441.69863.9632-0.00320.1163-0.3296-0.03330.2202-0.03580.23560.524-0.2170.24010.0046-0.01160.20860.07120.2591-47.25815.823.7763
33.4492-3.27241.43293.1698-1.54961.15640.0208-0.3734-0.0605-0.02450.31830.15290.0014-0.1067-0.33910.2611-0.0032-0.01740.12890.03920.2344-56.268125.03488.394
412.2288-11.38243.543912.151-6.878111.8919-0.2052-0.58370.67430.17630.1878-0.45010.4642-0.50350.01740.2566-0.17640.09080.6043-0.08110.3695-68.527324.46439.3454
51.8467-0.0896-0.85152.6167-0.4271.3439-0.0869-0.3702-0.1110.02230.10650.2340.1914-0.1244-0.01960.1159-0.0173-0.0470.17260.04140.0857-54.747632.28172.2397
65.98724.1721-1.51312.9464-0.98220.52270.1483-0.094-0.02140.2093-0.15860.00750.1271-0.15080.01030.2791-0.14670.0460.28550.0280.1156-61.96430.4246.022
74.9966-2.5385-2.01215.99812.8031.494-0.3335-0.5425-0.12820.17150.4747-0.42770.17720.3197-0.14130.20480.119-0.05730.19060.04730.1603-41.792524.65372.0449
88.0429-0.3771-0.12511.3664-0.41090.3308-0.01530.157-0.6696-0.41820.01970.03590.35650.0355-0.00450.38930.0344-0.0260.0758-0.01030.1649-48.447621.2743-7.5762
910.88693.5482-0.42563.1750.390.16360.10020.13410.2210.2244-0.06040.11920.0808-0.0405-0.03980.2601-0.02-0.03110.13740.07640.2671-58.98817.22660.7412
102.69451.36330.14553.5781-0.08361.5688-0.0340.2114-0.1581-0.08210.1141-0.02490.2684-0.0818-0.08010.12120.0154-0.03510.04610.00220.0794-56.669130.8643-10.6008
115.1055-4.26266.28274.7091-4.21148.68990.01260.2389-0.0206-0.17310.1128-0.1646-0.13750.5208-0.12540.0503-0.01550.03360.2544-0.09230.2308-34.769437.9805-11.0653
128.0745-4.44510.04633.0711.7455.21060.18830.010.1641-0.08070.1134-0.2688-0.00390.3353-0.30170.10810.0273-0.03560.1358-0.03880.2929-34.03440.9506-4.0148
131.18460.05260.43076.2057-0.70671.76390.095-0.25060.09240.12670.02060.107-0.00030.0608-0.11560.0452-0.0179-0.0220.0694-0.03650.0531-46.46146.84812.2747
147.8770.9087-1.42450.5236-0.9131.7760.1886-0.4274-0.0587-0.0218-0.1689-0.0376-0.09510.2904-0.01980.1812-0.0105-0.01220.07860.02690.1382-39.204634.31813.3578
153.9514-1.49282.74650.6144-0.95076.73090.09610.0271-0.1358-0.12680.0195-0.01390.11180.4268-0.11560.2141-0.00180.06460.0949-0.05810.1826-42.288630.2929-12.9004
165.9248-0.38567.71078.93131.71211.6068-0.00010.49460.0135-0.4034-0.287-0.1670.14280.31570.28710.1904-0.01580.02050.1514-0.06320.1702-55.321332.378-19.4708
172.85040.59840.29663.40281.24782.8455-0.08290.25820.0632-0.32530.10440.11260.11290.0717-0.02150.0980.0118-0.0450.03950.00310.0454-59.176437.5492-14.4353
186.94945.9031-2.89046.040.2828.5245-0.1127-0.02560.1068-0.24780.03620.133-0.31420.11380.07650.1610.027-0.04130.12270.00460.1021-59.407343.7932-20.5355
193.63680.65560.96971.67881.11722.22920.07-0.08910.0065-0.0959-0.01260.1143-0.0233-0.0088-0.05740.05280.0072-0.02070.00790.0110.0772-61.686741.5062-6.7818
2012.56333.583-4.00224.9628-4.64174.3852-0.1382-0.0756-0.3798-0.22540.28740.22060.2099-0.2484-0.14920.203-0.0136-0.01530.09090.00590.2458-73.309230.2331-4.6851
212.13145.13210.782412.94420.25284.9039-0.1237-0.0587-0.1225-0.2978-0.0621-0.3571-0.2182-0.20830.18580.13080.0042-0.03470.25730.01340.168-29.121515.7401-37.5653
223.8297-3.6825-0.94516.78295.69648.09990.3330.2465-0.0225-0.3764-0.0963-0.1096-0.5761-0.1717-0.23670.28410.0929-0.03830.31290.01560.2388-37.705726.8039-27.9413
232.20540.0904-0.09671.89671.47564.0136-0.00140.2343-0.0093-0.3943-0.07790.40570.0656-0.33460.07930.14180.0322-0.11940.27510.01130.1589-32.774811.886-29.2946
242.04990.3261-0.5143.76460.54311.4582-0.08040.32850.0367-0.18960.10040.04830.0779-0.2735-0.020.08720.0334-0.04810.18210.00980.0684-25.168114.9071-28.4251
250.15050.9761-1.04096.4804-6.93987.49990.06580.11940.08870.52020.62350.5102-0.6491-0.5462-0.68930.3062-0.0510.13660.4313-0.13960.5038-26.554633.2998-25.8488
261.51280.3220.59493.2854-0.02060.9067-0.09520.20560.0732-0.15170.05750.4079-0.0919-0.32320.03770.0460.033-0.03570.2765-0.01960.179-35.339517.4288-20.5283
276.62120.6137-1.20392.07680.09881.38010.11180.00160.14350.1262-0.04430.2597-0.0623-0.3553-0.06750.05140.0464-0.02260.1347-0.01870.0814-30.127914.8718-13.4951
286.21742.4063-1.97332.0893-0.37010.7605-0.13520.1553-0.1847-0.12820.01590.09180.0186-0.0580.11930.03340.0222-0.04240.14540.00390.0976-26.30229.6798-15.0043
293.3515.1285-2.93369.9383-6.2894.1363-0.0373-0.1321-0.04680.2078-0.0441-0.1484-0.23280.0170.08140.1582-0.00660.01440.1182-0.0620.1359-11.510523.7492-8.4857
304.6350.78753.01963.78331.4796.87760.06410.00330.396-0.2031-0.1098-0.3222-0.41140.22240.04570.25640.02340.03840.06080.01180.2088-11.364734.1721-18.1094
312.8559-0.8483-1.54581.51040.70545.2696-0.0281-0.04-0.0041-0.125-0.0760.0024-0.215-0.17970.10410.0340.0049-0.00260.04080.01690.0689-6.804417.932-23.7578
326.3901-6.38510.38186.4069-0.40110.08840.17880.16940.2065-0.1939-0.1368-0.1476-0.0653-0.0222-0.0420.16010.0167-0.01140.12160.06610.1406-11.662521.268-29.8292
330.7106-0.59130.99370.7212-0.61971.617-0.1630.03350.16890.1042-0.0508-0.1501-0.4022-0.04820.21380.26640.12070.02660.08510.02070.2607-19.809931.4142-20.0041
340.9057-1.7707-0.1515.8746-1.73473.80380.1467-0.10610.15620.21780.34240.4157-0.5145-0.0067-0.48910.18070.07370.12910.1203-0.01640.2772-22.73723.7537-7.1842
355.66951.36451.45034.777-1.75775.60730.0786-0.11720.24290.2648-0.08860.0003-0.167-0.39020.010.08170.05370.01420.1321-0.01880.0891-29.331712.689-4.0188
363.6304-0.9399-2.02671.9135-0.20572.4387-0.0182-0.1863-0.17120.0166-0.086-0.1054-0.0709-0.08080.10420.03810.0248-0.01640.08150.03080.0378-18.4717.4745-11.666
374.812.5827-3.84034.979-3.1796.8159-0.0032-0.1242-0.1773-0.0336-0.1525-0.1220.19090.15370.15560.09140.0367-0.03870.0859-0.01130.0977-13.76257.1047-3.9727
388.0883-0.6666-3.59532.80331.51562.72090.1876-0.28480.19470.45730.0051-0.0672-0.04330.0392-0.19260.13920.02360.01160.12430.030.0619-20.87023.4625-5.7351
391.78010.5820.56351.02080.37280.280.0101-0.1141-0.3991-0.26050.0907-0.2092-0.0837-0.0708-0.10080.0935-0.01160.00790.0911-0.02520.1202-15.32296.575-22.9766
401.1694-1.12612.47776.4477-1.40185.48370.1536-0.1295-0.22260.03030.18210.55430.4162-0.3458-0.33570.1359-0.05210.00590.2494-0.07360.2329-30.6184-2.0092-20.1934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection details
1X-RAY DIFFRACTION1ALL{ AAA|3-8 }
2X-RAY DIFFRACTION2ALL{ AAA|9-16 }
3X-RAY DIFFRACTION3ALL{ AAA|17-21 }
4X-RAY DIFFRACTION4ALL{ AAA|22-26 }
5X-RAY DIFFRACTION5ALL{ AAA|27-46 }
6X-RAY DIFFRACTION6ALL{ AAA|47-60 }
7X-RAY DIFFRACTION7ALL{ AAA|61-73 }
8X-RAY DIFFRACTION8ALL{ AAA|74-83 }
9X-RAY DIFFRACTION9ALL{ AAA|84-93 }
10X-RAY DIFFRACTION10ALL{ AAA|94-135 }
11X-RAY DIFFRACTION11ALL{ AAA|136-147 }
12X-RAY DIFFRACTION12ALL{ AAA|148-156 }
13X-RAY DIFFRACTION13ALL{ AAA|157-174 }
14X-RAY DIFFRACTION14ALL{ AAA|175-184 }
15X-RAY DIFFRACTION15ALL{ AAA|185-201 }
16X-RAY DIFFRACTION16ALL{ AAA|202-207 }
17X-RAY DIFFRACTION17ALL{ AAA|208-227 }
18X-RAY DIFFRACTION18ALL{ AAA|228-235 }
19X-RAY DIFFRACTION19ALL{ AAA|236-267 }
20X-RAY DIFFRACTION20ALL{ AAA|268-275 }
21X-RAY DIFFRACTION21ALL{ BBB|3-7 }
22X-RAY DIFFRACTION22ALL{ BBB|8-14 }
23X-RAY DIFFRACTION23ALL{ BBB|15-33 }
24X-RAY DIFFRACTION24ALL{ BBB|34-66 }
25X-RAY DIFFRACTION25ALL{ BBB|67-73 }
26X-RAY DIFFRACTION26ALL{ BBB|74-98 }
27X-RAY DIFFRACTION27ALL{ BBB|99-117 }
28X-RAY DIFFRACTION28ALL{ BBB|118-128 }
29X-RAY DIFFRACTION29ALL{ BBB|129-142 }
30X-RAY DIFFRACTION30ALL{ BBB|143-153 }
31X-RAY DIFFRACTION31ALL{ BBB|154-168 }
32X-RAY DIFFRACTION32ALL{ BBB|169-179 }
33X-RAY DIFFRACTION33ALL{ BBB|180-190 }
34X-RAY DIFFRACTION34ALL{ BBB|191-202 }
35X-RAY DIFFRACTION35ALL{ BBB|203-211 }
36X-RAY DIFFRACTION36ALL{ BBB|212-225 }
37X-RAY DIFFRACTION37ALL{ BBB|226-235 }
38X-RAY DIFFRACTION38ALL{ BBB|236-245 }
39X-RAY DIFFRACTION39ALL{ BBB|246-265 }
40X-RAY DIFFRACTION40ALL{ BBB|266-275 }

+
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