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- PDB-6s0s: The crystal structure of kanamycin B dioxygenase (KanJ) from Stre... -

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Basic information

Entry
Database: PDB / ID: 6s0s
TitleThe crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, ribostamycin B and 2-oxoglutarate
ComponentsKanamycin B dioxygenase
KeywordsMETAL BINDING PROTEIN / non-heme iron dioxygenase / alpha-ketoglutarate dioxygenase / Kanamycin biosynthesis / KanJ / OXIDOREDUCTASE / 2-oxoglutarate / ribostamycin B
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 / RIBOSTAMYCIN / Kanamycin B dioxygenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)195,10927
Polymers191,0476
Non-polymers4,06221
Water8,323462
1
A: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5004
Polymers31,8411
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5365
Polymers31,8411
Non-polymers6954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5365
Polymers31,8411
Non-polymers6954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5004
Polymers31,8411
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5365
Polymers31,8411
Non-polymers6954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5004
Polymers31,8411
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.083, 184.582, 110.333
Angle α, β, γ (deg.)90.00, 94.97, 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
11ALAALAPHEPHEAA2 - 2825 - 285
21ALAALAPHEPHEBB2 - 2825 - 285
12ALAALAHISHISAA2 - 2755 - 278
22ALAALAHISHISCC2 - 2755 - 278
13ALAALALEULEUAA2 - 2765 - 279
23ALAALALEULEUDD2 - 2765 - 279
14LEULEUHISHISAA3 - 2756 - 278
24LEULEUHISHISEE3 - 2756 - 278
15ALAALAHISHISAA2 - 2755 - 278
25ALAALAHISHISFF2 - 2755 - 278
16ALAALAHISHISBB2 - 2755 - 278
26ALAALAHISHISCC2 - 2755 - 278
17ALAALALEULEUBB2 - 2765 - 279
27ALAALALEULEUDD2 - 2765 - 279
18LEULEUHISHISBB3 - 2756 - 278
28LEULEUHISHISEE3 - 2756 - 278
19ALAALAHISHISBB2 - 2755 - 278
29ALAALAHISHISFF2 - 2755 - 278
110ALAALAHISHISCC0 - 2753 - 278
210ALAALAHISHISDD0 - 2753 - 278
111LEULEUHISHISCC3 - 2756 - 278
211LEULEUHISHISEE3 - 2756 - 278
112ALAALALEULEUCC0 - 2763 - 279
212ALAALALEULEUFF0 - 2763 - 279
113LEULEUHISHISDD3 - 2756 - 278
213LEULEUHISHISEE3 - 2756 - 278
114ALAALAHISHISDD0 - 2753 - 278
214ALAALAHISHISFF0 - 2753 - 278
115LEULEUHISHISEE3 - 2756 - 278
215LEULEUHISHISFF3 - 2756 - 278

NCS ensembles :
IDDetails
15E, F
1A, B
2A, C
3A, D
4A, E
5A, F
6B, C
7B, D
8B, E
9B, F
10C, D
11C, E
12C, F
13D, E
14D, F

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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: 31841.100 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 , 5 types, 483 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 454.473 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H34N4O10 / Comment: antibiotic*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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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: 5.29 Å3/Da / Density % sol: 76.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 of 28% PEG4000 (w/v), 0.2 M a-ketoglutaric acid disodium salt dihydrate, 0.1 M HEPES, 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: 2.4→47.27 Å / Num. obs: 67239 / % possible obs: 91.12 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Χ2: 0.974 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.863 / Num. unique obs: 3220 / Χ2: 0.717

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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: 2.4→47.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.701 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 3576 5 %RANDOM
Rwork0.17276 ---
obs0.17437 67239 91.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20.67 Å2
2--0.34 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13030 0 255 462 13747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313781
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712520
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.65118935
X-RAY DIFFRACTIONr_angle_other_deg1.2611.57229129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14851684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34221.563723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44151970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.30215102
X-RAY DIFFRACTIONr_chiral_restr0.0680.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022695
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_it2.0171.8796700
X-RAY DIFFRACTIONr_mcbond_other1.9861.8786699
X-RAY DIFFRACTIONr_mcangle_it3.1222.8138369
X-RAY DIFFRACTIONr_mcangle_other3.1292.8158370
X-RAY DIFFRACTIONr_scbond_it2.9272.1887081
X-RAY DIFFRACTIONr_scbond_other2.9272.1887082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2723.17310558
X-RAY DIFFRACTIONr_long_range_B_refined6.26123.22214049
X-RAY DIFFRACTIONr_long_range_B_other6.25323.1314003
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)
11A89070.07
12B89070.07
21A86910.06
22C86910.06
31A87740.06
32D87740.06
41A85120.07
42E85120.07
51A87110.06
52F87110.06
61B86110.06
62C86110.06
71B86820.07
72D86820.07
81B84460.08
82E84460.08
91B86410.07
92F86410.07
101C86220.08
102D86220.08
111C84630.07
112E84630.07
121C87000.06
122F87000.06
131D84580.08
132E84580.08
141D87010.07
142F87010.07
151E84760.07
152F84760.07
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.25 3330 -
obs--61.56 %
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)
12.73390.8413-2.3973.2749-0.91314.61230.2369-0.15950.64540.356-0.0998-0.5509-0.68820.6671-0.13710.3721-0.2215-0.14040.43220.0870.44793.01531.83499.543
217.58814.93791.019519.2379-0.1667.9677-0.23590.2457-0.3396-0.44150.21140.47340.1767-0.34190.02440.3496-0.0276-0.0180.29450.07010.1461-17.78413.44110.642
31.47270.078-0.16212.0763-0.24373.13860.0260.08060.03660.2926-0.2141-0.0331-0.07130.05610.18810.169-0.1473-0.03050.25580.04470.1182-5.94820.74896.878
42.5629-0.7101-0.51063.6411-0.93644.39290.12670.2081-0.3136-0.0917-0.2161-0.5720.79640.40350.08950.2654-0.0774-0.06290.41180.09410.29075.5813.11892.903
51.8892-0.25810.38092.08190.08122.34740.03370.10990.16720.3121-0.17620.4164-0.2312-0.36990.14240.2743-0.13370.03820.31290.01620.2139-14.924.96895.628
61.8442-0.7046-1.3125.2202-0.93163.19090.1214-0.04990.21450.162-0.02790.2273-0.1876-0.1249-0.09360.0916-0.00850.03540.0755-0.010.1327-9.8744.8633.756
71.34210.60330.33791.8374-0.43392.90340.03730.14280.0903-0.16230.0613-0.3239-0.1390.54-0.09850.1331-0.02820.05250.1173-0.0580.19467.3825.13323.262
81.48780.53490.43022.4714-0.44791.90280.01720.1553-0.1684-0.40650.1403-0.0470.09010.0378-0.15740.121-0.00060.00360.0234-0.0140.0604-3.064-6.36620.573
91.4271-0.33560.20223.00760.36161.82590.0060.03570.0049-0.10690.1022-0.1589-0.05030.2069-0.10810.0699-0.00770.0260.0251-0.01420.03161.736-2.28724.8
1010.05544.51096.22152.05822.78013.88980.87380.5534-1.46550.35340.0584-0.64620.41510.4284-0.93220.8190.2196-0.08451.1545-0.01280.676222.765-0.0220.906
118.03790.4122-0.614710.9847-1.08910.1641-0.6486-0.1011-0.4632-0.03340.7691.34-0.0095-0.1193-0.12040.60340.1641-0.15040.62090.06190.5596-5.04638.56940.448
122.3036-1.09740.37753.04350.06464.0456-0.0840.3389-0.0373-1.0459-0.04550.35350.2667-0.35470.12950.6279-0.1336-0.17650.15110.04360.12798.88537.42833.641
130.98230.19490.06082.5602-0.5123.5843-0.16790.07350.0931-0.77160.03770.1992-0.1669-0.23350.13030.4156-0.0394-0.19560.09670.03490.11799.2846.27436.406
144.3496-1.69342.95339.25882.33797.1645-0.04920.59230.1583-1.1506-0.0656-0.30510.35130.31950.11490.8728-0.0260.01870.26630.09130.107814.55142.06516.13
150.0462-0.0295-0.014616.56095.37241.74380.1477-0.115-0.1242-0.98540.0884-0.7666-0.33670.0429-0.23611.24280.0556-0.02670.96770.19210.74324.9833.62222.884
162.7798-1.87582.13213.54880.40045.68440.06950.0686-0.4569-0.00390.05340.08840.43810.2243-0.12280.25990.05040.09750.1270.00150.321640.15.47254.702
174.0242-5.2527-1.156410.5140.14361.1783-0.1041-0.0267-0.33190.1064-0.01790.63480.1536-0.09350.1220.2463-0.0425-0.01480.1802-0.0110.171117.96516.31254.963
181.93050.3030.43411.5553-0.22522.00430.036-0.3071-0.0441-0.1075-0.01360.09470.0186-0.0378-0.02240.1424-0.02590.04910.0645-0.01290.051631.30118.52361.206
193.83490.65161.25491.9536-0.10593.115-0.1509-0.15810.0701-0.20270.0838-0.2864-0.38860.41520.06720.2261-0.04470.08720.1123-0.01820.083541.59922.91455.541
204.51622.0176-0.19142.43910.90634.65680.1007-0.58160.02030.1552-0.27010.28810.0488-0.39210.16940.2041-0.03370.0770.28210.05930.190823.80714.14372.952
212.3243-0.2485-0.60792.86841.37524.45180.00470.19870.0886-1.3213-0.46881.1383-1.2379-0.93020.46421.07770.2547-0.65840.3773-0.25090.817315.679-14.59599.393
221.1445-0.3574-0.96683.70412.95285.4068-0.06590.0852-0.2015-1.4139-0.24230.6675-1.218-0.17690.30820.96280.0721-0.43080.1287-0.09370.343725.583-18.93596.88
233.09911.12692.50125.06161.0012.24370.3674-0.2384-0.42620.5605-0.0653-0.10030.5631-0.1046-0.3020.55150.0309-0.15530.10740.06430.226229.96146.95577.689
244.60721.485-2.77741.353-0.84855.58330.22150.0140.6175-0.0579-0.1010.6947-0.2758-0.8749-0.12040.2913-0.0444-0.0980.2916-0.07060.392611.65861.01563.879
251.7980.38160.78612.19391.14722.5570.1881-0.11210.07290.1817-0.021-0.02870.3712-0.1124-0.16720.1482-0.0441-0.07910.01710.02160.071626.72361.57474.056
262.31940.26430.53393.17941.14213.06410.16550.12840.0808-0.02350.0882-0.16790.20020.0743-0.25370.1647-0.0087-0.07990.02510.01980.078428.10759.74868.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 56
2X-RAY DIFFRACTION2A57 - 69
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