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- PDB-6cx8: Crystal structure of spermidine/spermine N-acetyltransferase SpeG... -

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Basic information

Entry
Database: PDB / ID: 6cx8
TitleCrystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.
ComponentsSpermidine N(1)-acetyltransferase
KeywordsTRANSFERASE / SpeG / spermidine / GNAT / N-acetyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


spermidine catabolic process / polyamine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / : / PHOSPHATE ION / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_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: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,69717
Polymers125,8546
Non-polymers84311
Water3,711206
1
A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,39434
Polymers251,70812
Non-polymers1,68622
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area36310 Å2
ΔGint-137 kcal/mol
Surface area83600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.645, 135.267, 73.675
Angle α, β, γ (deg.)90.00, 118.58, 90.00
Int Tables number5
Space group name H-MC121
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 1694 - 172
21METMETLEULEUBB1 - 1694 - 172
12ASNASNLEULEUAA2 - 1695 - 172
22ASNASNLEULEUCC2 - 1695 - 172
13ASNASNLEULEUAA2 - 1695 - 172
23ASNASNLEULEUDD2 - 1695 - 172
14METMETGLUGLUAA1 - 1734 - 176
24METMETGLUGLUEE1 - 1734 - 176
15ASNASNLEULEUAA2 - 1695 - 172
25ASNASNLEULEUFF2 - 1695 - 172
16ASNASNLEULEUBB2 - 1695 - 172
26ASNASNLEULEUCC2 - 1695 - 172
17ASNASNLEULEUBB2 - 1695 - 172
27ASNASNLEULEUDD2 - 1695 - 172
18METMETASNASNBB1 - 1704 - 173
28METMETASNASNEE1 - 1704 - 173
19ASNASNLEULEUBB2 - 1695 - 172
29ASNASNLEULEUFF2 - 1695 - 172
110ASNASNASNASNCC2 - 1705 - 173
210ASNASNASNASNDD2 - 1705 - 173
111ASNASNLEULEUCC2 - 1695 - 172
211ASNASNLEULEUEE2 - 1695 - 172
112ASNASNASNASNCC2 - 1705 - 173
212ASNASNASNASNFF2 - 1705 - 173
113ASNASNLEULEUDD2 - 1695 - 172
213ASNASNLEULEUEE2 - 1695 - 172
114ASNASNASNASNDD2 - 1705 - 173
214ASNASNASNASNFF2 - 1705 - 173
115ASNASNLEULEUEE2 - 1695 - 172
215ASNASNLEULEUFF2 - 1695 - 172

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
Spermidine N(1)-acetyltransferase / SAT / Spermidine/spermine N(1)-acetyltransferase / SSAT


Mass: 20975.646 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: speG, VC_A0947 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q9KL03, diamine N-acetyltransferase

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Non-polymers , 5 types, 217 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide, 0.1 M Tris, 20% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2016 / Details: Beryllium Lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 49284 / % possible obs: 94.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.7
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2519 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCZ
Resolution: 2.41→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 16.384 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21319 2363 4.8 %RANDOM
Rwork0.17137 ---
obs0.17346 46921 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-1.61 Å2
2--0.13 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.41→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 43 206 8865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198919
X-RAY DIFFRACTIONr_bond_other_d0.0010.028021
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.93812030
X-RAY DIFFRACTIONr_angle_other_deg1.073318541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.73451025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.58624.093535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.755151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8321568
X-RAY DIFFRACTIONr_chiral_restr0.1420.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.029973
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021964
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_it4.1833.5984103
X-RAY DIFFRACTIONr_mcbond_other4.183.5974102
X-RAY DIFFRACTIONr_mcangle_it5.6265.3855127
X-RAY DIFFRACTIONr_mcangle_other5.6265.3855128
X-RAY DIFFRACTIONr_scbond_it5.5924.0394816
X-RAY DIFFRACTIONr_scbond_other5.5914.044817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5475.8946904
X-RAY DIFFRACTIONr_long_range_B_refined9.22241.5749955
X-RAY DIFFRACTIONr_long_range_B_other9.22641.5359939
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)
11A114980.07
12B114980.07
21A114720.07
22C114720.07
31A114200.07
32D114200.07
41A112100.08
42E112100.08
51A112720.08
52F112720.08
61B113220.07
62C113220.07
71B112580.07
72D112580.07
81B107720.08
82E107720.08
91B111760.08
92F111760.08
101C114340.07
102D114340.07
111C107980.08
112E107980.08
121C111980.09
122F111980.09
131D108820.08
132E108820.08
141D111860.08
142F111860.08
151E105740.09
152F105740.09
LS refinement shellResolution: 2.406→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 150 -
Rwork0.289 3372 -
obs--89.94 %
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)
14.1903-0.74740.48912.92390.7532.7809-0.02860.02310.1652-0.3846-0.1175-0.50970.1820.50520.14620.19740.10730.10260.29270.07820.2256130.618859.643284.526
20.25480.61210.43854.0492-0.86142.455-0.05810.0134-0.0013-0.19030.08550.17680.04210.0441-0.02740.06470.0212-0.00450.1114-0.02980.1402117.224858.3691.0313
31.05810.4870.61682.9427-3.34085.2229-0.08670.1437-0.115-0.5473-0.2555-0.380.65790.57370.34230.14570.10710.02030.18440.01250.1776130.561657.189394.471
42.5998-0.01422.60191.21230.73975.53910.04950.1765-0.2156-0.2153-0.1949-0.27750.18430.71510.14540.10640.15830.05460.28190.110.2601135.924652.050892.4177
55.38361.35520.57751.1370.2010.7872-0.16450.2367-0.4565-0.09980.1093-0.17580.19660.2650.05510.14540.12240.03580.15460.03590.2197130.308541.636499.9198
63.0866-0.68560.47351.5987-0.0891.84430.0125-0.3817-0.17790.0938-0.03630.0580.03660.01780.02380.04310.008-0.03060.12170.04650.0676108.07158.3255116.358
72.5292-1.1156-2.92222.56773.16416.6943-0.1711-0.2957-0.38080.13920.14520.11320.5548-0.02890.02590.1137-0.0109-0.05010.15770.12520.1777105.832848.7791113.6651
82.8692-0.5551-1.67077.8007-3.21527.95940.273-0.1842-0.10480.3678-0.3114-0.19660.07680.09050.03840.15860.0489-0.00280.22250.12670.1039108.401845.4939126.0114
95.76561.45372.86190.36880.72774.4255-0.0032-0.3453-0.4225-0.012-0.1012-0.11250.3598-0.0420.10440.17950.0616-0.02740.09670.10530.2379111.32440.5874113.6459
104.08422.58370.02232.38830.4981.56850.0102-0.3108-0.52980.2147-0.0781-0.0970.36120.27290.06790.18390.09790.0120.14020.13370.2835119.737340.2294113.7455
113.2910.30240.00332.64420.39521.50230.0898-0.55310.06090.2845-0.11040.2217-0.12380.20570.02060.1004-0.06380.00030.2121-0.02720.037118.54978.5972122.5162
126.3385-2.4808-3.31351.86410.42092.654-0.2211-0.6356-0.17770.14690.03930.01790.14330.48640.18180.1567-0.0607-0.01230.27870.01530.1246127.262671.5865121.1046
134.3994-4.1295-0.02036.03552.55178.299-0.2816-0.65260.08470.51830.1948-0.166-0.10860.38840.08690.0869-0.096-0.02380.38140.01770.0169127.524773.7865134.1929
141.27290.2945-0.48573.6850.2641.36750.0882-0.4026-0.08590.52030.0274-0.2030.0180.564-0.11560.1463-0.0305-0.08790.45680.00060.0751137.948776.3089125.4225
150.93310.71660.17764.10930.95091.4074-0.0674-0.2939-0.12210.39490.3694-0.35370.01650.2951-0.3020.1817-0.0114-0.12810.5594-0.00360.206140.376873.9518124.2069
165.28671.05920.76287.2662-0.51471.8418-0.00280.06830.1749-0.3593-0.1617-0.407-0.10980.54410.16440.0471-0.06980.02930.26340.01360.0533137.884582.635789.3567
173.5182-1.0881.63642.20582.15124.5495-0.0512-0.194-0.1695-0.03410.07650.099-0.0932-0.0286-0.02540.0423-0.0415-0.02030.1270.01720.051129.914676.643197.8089
180.95680.3863-1.01641.3078-0.24018.03110.0008-0.1260.20560.00110.0517-0.344-0.00420.7171-0.05250.0214-0.0528-0.00820.2015-0.02720.2127139.079186.371798.7384
194.6459-1.0225-2.85375.87574.23015.90690.0537-0.0213-0.0059-0.2945-0.0234-0.4557-0.42090.7537-0.03030.0452-0.10360.02030.42870.02210.1704148.39185.680395.6037
200.68370.3534-0.7125.2389-1.03141.90410.0099-0.3089-0.0164-0.0291-0.0459-0.5584-0.07220.51110.0360.0398-0.0586-0.04630.4206-0.03840.1779147.626481.2146109.6333
214.68791.6341-1.06762.6098-0.97891.19550.1105-0.28770.39490.0731-0.01220.4087-0.26150.0427-0.09830.1174-0.04930.01080.1326-0.10150.1564111.9669100.3177117.2874
2212.427-3.3448-10.05330.95463.035511.729-0.0957-0.19790.0241-0.0330.00460.0266-0.3989-0.01260.0910.1903-0.02770.07180.1012-0.09970.1126111.2344109.9829124.274
232.52441.11460.00111.6953-0.3021.69340.3778-0.70930.40250.4664-0.33420.1921-0.5010.1916-0.04350.373-0.220.10580.3979-0.27580.2106123.2249111.6461122.3305
241.3896-1.15933.82781.0159-3.20110.5621-0.2645-0.17060.08230.36990.12130.0351-0.7007-0.44860.14320.6054-0.01510.26580.1653-0.18880.4889114.2261122.7576108.4416
253.7926-2.78962.50862.7883-2.21894.04720.0077-0.35860.49170.6488-0.0577-0.1977-0.58440.15750.050.6158-0.28580.11880.2681-0.23670.2738129.1075113.3621118.8871
263.0602-1.522-0.27635.7967-1.09674.0363-0.13850.47980.2001-0.36180.015-0.0507-0.08850.06110.12350.0706-0.0679-0.04260.176-0.00180.106125.5141104.00783.208
273.96340.23190.42726.75571.65041.38790.1706-0.0327-0.01380.4232-0.28790.33260.1270.00790.11730.0547-0.04830.02190.0951-0.05110.06121.708197.663694.1687
283.06031.6914-2.56663.6799-0.81183.3499-0.03440.25120.33-0.3118-0.07170.309-0.2681-0.05650.10610.0833-0.0311-0.09120.17020.02790.192124.8899111.712387.0009
294.0573-1.6240.5293.3107-0.33382.4230.15620.2370.55320.191-0.24830.4534-0.39980.15080.09210.1174-0.05560.08240.1039-0.03830.277125.0664118.971793.6021
303.1794-2.32911.33524.9984-1.97762.7224-0.0759-0.04660.55040.2964-0.1414-0.1913-0.40260.23420.21740.1723-0.14840.06040.1362-0.08640.2175129.5103118.4507101.1254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A24 - 55
3X-RAY DIFFRACTION3A56 - 85
4X-RAY DIFFRACTION4A86 - 117
5X-RAY DIFFRACTION5A118 - 173
6X-RAY DIFFRACTION6B1 - 58
7X-RAY DIFFRACTION7B59 - 85
8X-RAY DIFFRACTION8B86 - 102
9X-RAY DIFFRACTION9B103 - 132
10X-RAY DIFFRACTION10B133 - 170
11X-RAY DIFFRACTION11C2 - 64
12X-RAY DIFFRACTION12C65 - 85
13X-RAY DIFFRACTION13C86 - 108
14X-RAY DIFFRACTION14C109 - 153
15X-RAY DIFFRACTION15C154 - 170
16X-RAY DIFFRACTION16D2 - 23
17X-RAY DIFFRACTION17D24 - 56
18X-RAY DIFFRACTION18D57 - 87
19X-RAY DIFFRACTION19D88 - 111
20X-RAY DIFFRACTION20D112 - 170
21X-RAY DIFFRACTION21E0 - 84
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