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- PDB-6s0u: The crystal structure of kanamycin B dioxygenase (KanJ) from Stre... -

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Basic information

Entry
Database: PDB / ID: 6s0u
TitleThe crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and 2-oxoglutarate
ComponentsKanamycin B dioxygenase
KeywordsMETAL BINDING PROTEIN / non-heme iron dioxygenase / alpha-ketoglutarate dioxygenase / Kanamycin biosynthesis / KanJ / OXIDOREDUCTASE / 2-oxoglutarate
Function / homology
Function and homology information


kanamycin B dioxygenase / kanamycin biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity
Similarity search - Function
: / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH)
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Kanamycin B dioxygenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsMrugala, B. / Porebski, P.J. / Niedzialkowska, E. / Minor, W. / Borowski, T.
Funding support Poland, United States, 2items
OrganizationGrant numberCountry
Polish National Science Centre2014/15/B/NZ1/03331 Poland
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-GM117325-01 United States
CitationJournal: Febs J. / Year: 2021
Title: A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Authors: Mrugala, B. / Milaczewska, A. / Porebski, P.J. / Niedzialkowska, E. / Guzik, M. / Minor, W. / Borowski, T.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kanamycin B dioxygenase
B: Kanamycin B dioxygenase
C: Kanamycin B dioxygenase
D: Kanamycin B dioxygenase
E: Kanamycin B dioxygenase
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,76723
Polymers185,2326
Non-polymers1,53517
Water20,9151161
1
A: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0773
Polymers30,8721
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1834
Polymers30,8721
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1124
Polymers30,8721
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0773
Polymers30,8721
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1355
Polymers30,8721
Non-polymers2634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1834
Polymers30,8721
Non-polymers3113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.825, 183.691, 110.169
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAHISHISAA2 - 2754 - 277
21ALAALAHISHISBB2 - 2754 - 277
12ALAALAHISHISAA2 - 2754 - 277
22ALAALAHISHISCC2 - 2754 - 277
13ALAALAHISHISAA2 - 2754 - 277
23ALAALAHISHISDD2 - 2754 - 277
14ALAALAHISHISAA2 - 2754 - 277
24ALAALAHISHISEE2 - 2754 - 277
15ALAALAASPASPAA2 - 2744 - 276
25ALAALAASPASPFF2 - 2744 - 276
16ALAALAHISHISBB2 - 2754 - 277
26ALAALAHISHISCC2 - 2754 - 277
17ALAALAHISHISBB2 - 2754 - 277
27ALAALAHISHISDD2 - 2754 - 277
18ALAALALEULEUBB2 - 2764 - 278
28ALAALALEULEUEE2 - 2764 - 278
19ALAALAASPASPBB2 - 2744 - 276
29ALAALAASPASPFF2 - 2744 - 276
110METMETHISHISCC1 - 2753 - 277
210METMETHISHISDD1 - 2753 - 277
111ALAALAHISHISCC2 - 2754 - 277
211ALAALAHISHISEE2 - 2754 - 277
112METMETASPASPCC1 - 2743 - 276
212METMETASPASPFF1 - 2743 - 276
113ALAALAHISHISDD2 - 2754 - 277
213ALAALAHISHISEE2 - 2754 - 277
114METMETASPASPDD1 - 2743 - 276
214METMETASPASPFF1 - 2743 - 276
115ALAALAASPASPEE2 - 2744 - 276
215ALAALAASPASPFF2 - 2744 - 276

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Kanamycin B dioxygenase / Kanamycin biosynthesis protein J


Mass: 30872.049 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: kanJ, kacB / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): MAGIC / References: UniProt: Q6L732, kanamycin B dioxygenase

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Non-polymers , 6 types, 1178 molecules

#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.21 Å3/Da / Density % sol: 76.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 of 25% PEG4000, 0.2 M alpha-Ketoglutaric acid disodium salt dihydrate, 0.05 M bis-tris methane, 0.15 M NaCl and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2017 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→45.73 Å / Num. obs: 105045 / % possible obs: 92.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.179 / Χ2: 0.872 / Net I/σ(I): 6.2
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.69 / Num. unique obs: 5177 / CC1/2: 0.579 / Χ2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6S0T
Resolution: 2.15→45.73 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 13.221 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24429 4839 4.9 %RANDOM
Rwork0.19581 ---
obs0.1982 93360 92.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å20.47 Å2
2---1.2 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.15→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12906 0 83 1161 14150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313482
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712276
X-RAY DIFFRACTIONr_angle_refined_deg1.541.64918538
X-RAY DIFFRACTIONr_angle_other_deg1.3411.56628534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2951675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70321.421725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.079151970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.15515106
X-RAY DIFFRACTIONr_chiral_restr0.080.21711
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022682
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6851.2336652
X-RAY DIFFRACTIONr_mcbond_other1.6851.2346651
X-RAY DIFFRACTIONr_mcangle_it2.591.8428316
X-RAY DIFFRACTIONr_mcangle_other2.591.8428317
X-RAY DIFFRACTIONr_scbond_it2.3921.4266830
X-RAY DIFFRACTIONr_scbond_other2.3931.4276831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5452.05510214
X-RAY DIFFRACTIONr_long_range_B_refined6.56215.7614722
X-RAY DIFFRACTIONr_long_range_B_other6.56215.76514723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87260.07
12B87260.07
21A87510.08
22C87510.08
31A87960.06
32D87960.06
41A87930.06
42E87930.06
51A86740.07
52F86740.07
61B86920.09
62C86920.09
71B86890.08
72D86890.08
81B87590.08
82E87590.08
91B85810.09
92F85810.09
101C88070.08
102D88070.08
111C88090.08
112E88090.08
121C87240.09
122F87240.09
131D88400.07
132E88400.07
141D87660.08
142F87660.08
151E87730.07
152F87730.07
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 307 -
Rwork0.239 5843 -
obs--78.52 %
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)
15.65940.66611.6975.592.4654.82060.16840.21120.8643-0.3481-0.40570.7654-0.6276-0.55960.23730.38090.2266-0.14670.3188-0.13250.382727.17656.26364.617
23.7464-2.3991-1.16721.69930.88794.18610.14410.10330.3344-0.2162-0.15240.1266-0.486-0.32390.00830.42870.0913-0.19560.3801-0.16780.754929.28754.60569.011
33.247-0.5225-0.81740.7951.37412.3956-0.06120.2224-0.1293-0.04670.162-0.067-0.11820.2364-0.10090.37210.0298-0.03260.2599-0.0790.044447.37438.86756.338
41.22680.24140.35921.80260.53141.27850.0658-0.08330.0651-0.2035-0.18910.269-0.086-0.16290.12330.21080.0525-0.03870.2191-0.08080.054435.39641.48568.546
52.89440.9734-0.23935.3575-3.25743.9086-0.08660.1374-0.0891-0.1862-0.1384-0.5040.01690.34360.22510.19680.0073-0.00060.2058-0.05580.126853.41450.68372.594
61.6117-0.2765-0.37492.55590.49911.19730.0689-0.01030.0693-0.12560.0578-0.1944-0.15940.1823-0.12670.255-0.02250.04750.2286-0.00950.032143.65826.499130.772
76.40072.1748-5.38153.4835-3.09359.9880.09940.13820.3944-0.1478-0.01430.0176-0.0851-0.5306-0.08510.2320.0624-0.03850.1355-0.05460.093823.2635.994144.675
80.9199-0.53610.00411.91150.62031.49380.0172-0.0326-0.06660.120.0460.0265-0.0778-0.0349-0.06330.2169-0.010500.1754-0.00720.008531.7920.27141.302
91.2753-0.08250.27421.04380.23961.18870.0358-0.0027-0.02160.0582-0.0350.0414-0.1051-0.0397-0.00070.21690.00690.01270.1610.00010.002530.15320.389140.127
103.00071.55980.55041.68240.56111.96390.0184-0.1227-0.33280.27860.0853-0.44040.36020.2974-0.10370.30550.1348-0.10590.2329-0.03750.124332.02360.497130.462
110.42260.48030.12391.77710.431.55280.032-0.07460.0420.25590.07810.01050.1924-0.0107-0.11020.24760.057-0.03560.2003-0.01220.016721.50166.764129.894
124.3085-2.65890.39024.61441.29252.198-0.15210.13550.55570.00710.03490.0236-0.4343-0.16760.11710.20870.0481-0.02070.19080.00640.151218.64182.737117.959
130.60240.0045-0.0261.5970.45931.350.0285-0.03220.04590.19720.0362-0.16840.25380.0188-0.06460.19690.0242-0.06070.1954-0.02070.033323.30566.896129.36
146.7846-0.50371.17595.5470.22984.33470.10940.0338-0.17140.6921-0.13020.62560.7117-0.4060.02090.5105-0.034-0.01060.3227-0.02480.097217.18562.109146.833
151.56130.564-0.19711.65210.03811.39780.02260.0414-0.39250.22350.0213-0.06720.2144-0.0188-0.04380.28070.01110.01070.1430.00260.11232.54332.983109.613
161.38690.02650.1870.71610.01291.66930.04360.1578-0.08960.1163-0.0507-0.01070.0366-0.06070.00720.2360.00270.04110.1586-0.00370.01570.83541.213103.389
1712.12622.4408-0.56835.37680.43216.7366-0.3870.51470.7986-0.40340.21610.3997-0.6659-0.20850.17080.27880.03550.00920.23360.04190.1142-12.99954.44101.794
181.54140.18150.36831.3194-0.21621.66770.0408-0.0462-0.05970.2543-0.04390.0271-0.0276-0.13640.00310.26540.00440.07450.1717-0.01130.0272-3.88442.267110.051
195.3593-1.82180.50641.5017-0.99582.5371-0.00270.42660.2014-0.0794-0.0637-0.19430.22770.4360.06650.23710.05830.0390.2901-0.07270.069911.25836.12590.481
202.01370.72850.27522.6071-0.4222.5978-0.0294-0.21060.14110.3034-0.1053-0.1114-0.4337-0.02690.13460.326-0.0197-0.10010.192-0.04580.050614.08416.85278.131
215.4992.19154.49577.54825.616110.58530.17940.2541-0.1742-0.1456-0.2114-0.14040.08020.16930.0320.14960.02820.04910.19270.09990.118120.3265.8553.774
220.9787-0.071-0.07660.7921-0.46991.3566-0.046-0.0237-0.07470.0563-0.007-0.0353-0.0754-0.01060.0530.2221-0.0279-0.05770.14530.0330.04736.866.8567.422
237.71281.4829-1.96872.1057-0.30571.624-0.1257-0.0146-0.48050.0278-0.0672-0.30880.17680.12530.19290.19430.0439-0.04790.14380.08070.168820.985-7.49672.016
240.08470.3799-0.402815.4938-23.196535.2766-0.13670.3329-0.23390.44081.70730.7959-1.2093-1.6615-1.57061.6093-0.49920.78471.7645-0.50021.299424.211-8.26856.834
252.0283-0.14130.87431.439-0.53541.82250.13310.2845-0.2405-0.2772-0.05740.1690.49280.0905-0.07580.38310.0284-0.02510.2456-0.02690.06671.83769.44386.268
261.2525-0.15841.15860.5785-0.32471.75030.04490.17720.1328-0.0948-0.0341-0.06320.06750.3196-0.01090.22260.02240.03170.25470.01830.06111.30983.48493.502
271.1932-0.6740.40951.335-0.13061.76680.0173-0.1084-0.05460.05160.05510.08370.1675-0.0321-0.07250.1848-0.0080.02350.16290.00340.02510.94679.263100.433
284.7997-1.8549-2.01163.7821.50351.8940.01280.20940.4612-0.4297-0.0326-0.3195-0.12550.44630.01980.2694-0.03210.01930.42350.15090.121713.97191.12480.443
2933.06532.936234.48640.31763.064336.24631.49832.3757-1.69690.1530.4115-0.14550.92422.4085-1.90981.60340.37570.72230.84410.05832.284226.51692.16289.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 22
2X-RAY DIFFRACTION2A23 - 48
3X-RAY DIFFRACTION3A49 - 80
4X-RAY DIFFRACTION4A81 - 239
5X-RAY DIFFRACTION5A240 - 277
6X-RAY DIFFRACTION6B2 - 45
7X-RAY DIFFRACTION7B46 - 67
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