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- PDB-6dau: Crystal structure of E33Q and E41Q mutant forms of the spermidine... -

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Basic information

Entry
Database: PDB / ID: 6dau
TitleCrystal structure of E33Q and E41Q mutant forms of the spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae
ComponentsSpermidine N1-acetyltransferase
KeywordsTRANSFERASE / SpeG / polyamine / GNAT / N-acetyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


polyamine catabolic process / spermidine 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
: / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFilippova, E.V. / Minasov, G. / Beahan, A. / Kulyavtsev, P. / Tan, L. / Tran, D. / Kuhn, M.L. / 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 E33Q and E41Q mutant forms of the spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae.
Authors: Filippova, E.V. / Minasov, G. / Beahan, A. / Kulyavtsev, P. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
E: Spermidine N1-acetyltransferase
F: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4859
Polymers124,2086
Non-polymers2763
Water3,909217
1
A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
hetero molecules

E: Spermidine N1-acetyltransferase

E: Spermidine N1-acetyltransferase

F: Spermidine N1-acetyltransferase

F: Spermidine N1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)248,97018
Polymers248,41712
Non-polymers5536
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
crystal symmetry operation3_444x-1/2,y-1/2,z-11
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area30000 Å2
ΔGint-65 kcal/mol
Surface area88140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.235, 133.016, 77.711
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

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
11SERSERLEULEUAA3 - 1693 - 169
21SERSERLEULEUBB3 - 1693 - 169
12ASNASNASNASNAA2 - 1702 - 170
22ASNASNASNASNCC2 - 1702 - 170
13ASNASNASNASNAA2 - 1702 - 170
23ASNASNASNASNDD2 - 1702 - 170
14GLNGLNARGARGAA4 - 1714 - 171
24GLNGLNARGARGEE4 - 1714 - 171
15GLNGLNLEULEUAA4 - 1694 - 169
25GLNGLNLEULEUFF4 - 1694 - 169
16SERSERLEULEUBB3 - 1693 - 169
26SERSERLEULEUCC3 - 1693 - 169
17SERSERLEULEUBB3 - 1693 - 169
27SERSERLEULEUDD3 - 1693 - 169
18GLNGLNASNASNBB4 - 1704 - 170
28GLNGLNASNASNEE4 - 1704 - 170
19GLNGLNLEULEUBB4 - 1694 - 169
29GLNGLNLEULEUFF4 - 1694 - 169
110ASNASNARGARGCC2 - 1712 - 171
210ASNASNARGARGDD2 - 1712 - 171
111GLNGLNGLUGLUCC4 - 1734 - 173
211GLNGLNGLUGLUEE4 - 1734 - 173
112GLNGLNLEULEUCC4 - 1694 - 169
212GLNGLNLEULEUFF4 - 1694 - 169
113GLNGLNGLUGLUDD4 - 1734 - 173
213GLNGLNSERSEREE4 - 1724 - 172
114GLNGLNLEULEUDD4 - 1694 - 169
214GLNGLNLEULEUFF4 - 1694 - 169
115GLNGLNASNASNEE4 - 1704 - 170
215GLNGLNASNASNFF4 - 1704 - 170

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

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Components

#1: Protein
Spermidine N1-acetyltransferase


Mass: 20701.416 Da / Num. of mol.: 6 / Mutation: E33Q, E41Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Gene: C4E16_17415 / Plasmid: MCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2L2MBX3, UniProt: Q9KL03*PLUS, diamine N-acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01 M magnesium chloride, 0.1 M Tris, 10% isopropanol

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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: Apr 11, 2017 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. obs: 68104 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.2
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CNP
Resolution: 2.26→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 13.282 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3393 5 %RANDOM
Rwork0.189 ---
obs0.19 64711 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å21.46 Å2
2---3.02 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8569 0 18 217 8804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.93411963
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63451020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60124.007534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.941151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9471570
X-RAY DIFFRACTIONr_chiral_restr0.1120.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026934
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.685.1154083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0097.6455102
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4375.3634776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.15767.43412814
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A113460.06
12B113460.06
21A114800.06
22C114800.06
31A115020.06
32D115020.06
41A109900.06
42E109900.06
51A111760.06
52F111760.06
61B112440.05
62C112440.05
71B113120.04
72D113120.04
81B108700.05
82E108700.05
91B112120.05
92F112120.05
101C115100.05
102D115100.05
111C110860.07
112E110860.07
121C111100.06
122F111100.06
131D108980.06
132E108980.06
141D111760.06
142F111760.06
151E106880.06
152F106880.06
LS refinement shellResolution: 2.27→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 239 -
Rwork0.286 4514 -
obs--93.82 %
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)
12.650.02440.45596.5165-1.39673.6470.13660.2759-0.1203-0.3617-0.04990.0702-0.0250.3236-0.08670.0866-0.02840.01010.0922-0.00420.04632.893554.811320.1231
24.05530.9812.54627.2938-1.65662.3392-0.25730.319-0.0545-0.01570.2171-0.0866-0.19610.17540.04010.1995-0.0471-0.02130.2233-0.01390.17687.245752.142934.2542
31.99540.3881-0.65842.69520.21071.3008-0.01790.1166-0.0602-0.19550.15730.07330.09180.1465-0.13940.046-0.0246-0.04610.0927-0.00360.12610.345151.608826.1774
43.0290.2514-1.01121.34290.12271.20790.0253-0.05790.288-0.05150.062-0.0392-0.29810.1373-0.08730.101-0.050.01790.0638-0.010.22471.322166.423629.9571
54.4228-0.75991.16753.8011-0.14965.14860.01050.00970.80150.01320.0139-0.3215-0.58410.3621-0.02440.1169-0.08940.06540.0776-0.07830.33859.298373.386736.659
65.438-2.72582.90412.8489-2.41362.61190.09320.08430.8782-0.1843-0.2981-0.33690.01880.34840.20490.1529-0.07850.05140.1391-0.06280.32496.097469.200838.0479
75.4522.0481-0.49116.30480.46083.8355-0.182-0.0088-0.0352-0.7048-0.03760.06550.23450.3370.21960.16350.07350.04180.1570.03670.031417.290632.776329.7494
81.87-0.4047-1.44536.4896-0.43582.0174-0.0751-0.2333-0.079-0.3511-0.09930.01850.22960.09380.17450.10710.06370.00320.15560.01910.06139.209127.832138.7474
91.8780.60570.68912.07750.38992.0747-0.0110.04650.0465-0.183-0.0965-0.249-0.01610.33950.10750.02910.05510.02890.23350.05670.058718.901637.903738.3813
106.46521.7227-0.1835.28053.84523.344-0.22720.1629-0.3884-0.6540.2553-0.4431-0.42260.429-0.02810.18880.08050.10330.54230.17620.406631.215935.913332.0644
111.767-0.61831.59454.4971-0.81922.1386-0.00580.03960.1159-0.2559-0.2198-0.5204-0.05060.40030.22570.03070.00280.04180.33190.0580.160127.61839.948745.304
121.48790.6135-0.19696.2587-0.98311.4453-0.2379-0.202-0.09240.11350.0992-1.01180.09640.26780.13870.0550.0401-0.01850.38480.03010.201127.417232.351351.7079
136.5724-0.39542.46172.94670.62623.63760.0338-0.9235-0.15860.34240.19180.1679-0.2243-0.1064-0.22560.13540.03640.0290.3535-0.10110.0987-11.023751.478964.1391
149.1098-1.49894.990616.5563-15.523715.98910.1441-0.771-0.04570.5505-0.3939-0.2863-0.45420.04250.24980.294-0.0331-0.03930.129-0.06390.1356-17.182963.428455.4884
153.4105-0.55480.0832.8950.53362.68440.0794-0.21520.04940.07730.11330.2435-0.11130.2079-0.19270.01740.01090.00310.1223-0.0870.1034-10.747850.753855.3055
164.8578-1.1205-1.65542.64071.16423.05150.0706-0.46360.45110.1955-0.0710.0536-0.3420.2680.00050.0933-0.0358-0.0110.2191-0.160.1432-1.344959.258660.4267
174.4612-1.96430.3264.9677-0.94831.7833-0.0211-0.63480.41120.378-0.004-0.1234-0.28660.14890.02510.1023-0.08020.01940.2935-0.19880.15443.257565.555858.2227
185.2964-0.93372.59552.249-1.59222.5111-0.0244-0.61560.79380.3742-0.0341-0.1253-0.3301-0.0550.05850.1321-0.07290.0570.215-0.20980.29381.641468.934453.0445
195.1436-1.28842.37077.4371-2.32593.9311-0.0669-0.12560.00840.64510.00890.4943-0.42410.17580.05790.17240.03450.06160.3713-0.02530.0729-0.437730.151470.5582
201.797-0.25240.93193.6416-0.67672.04610.087-0.2861-0.03140.0729-0.13290.4465-0.0157-0.09030.04590.03910.0689-0.00370.3003-0.03730.06820.066230.941162.6007
213.4016-2.0248-2.7243.58790.91025.1360.0477-0.459-0.0620.0544-0.1479-0.2426-0.07990.3190.10020.02430.0365-0.00920.30160.0630.034411.780526.10561.4115
222.3637-0.0159-0.3473.8860.83181.5792-0.027-0.6678-0.19120.5376-0.1239-0.2847-0.00610.15450.15090.19080.0639-0.06150.52940.07930.062214.216725.654470.1729
231.3747-1.1313-0.22196.7815-2.32161.781-0.1248-0.37770.18080.76870.0148-0.6941-0.28770.24450.110.13420.0255-0.10410.4349-0.02610.10721.743137.199366.1195
245.2101-0.96052.82753.2346-2.83493.64420.0991-0.3013-0.76950.4335-0.0294-0.4496-0.01780.2173-0.06970.29130.1794-0.1630.57090.09480.367922.623118.341866.5329
256.65410.2696-1.13766.65230.48515.2688-0.1218-0.3957-0.24681.3822-0.1802-0.15050.7640.04070.3020.4874-0.0963-0.01020.06690.02870.0341.627376.337243.579
265.245-1.2450.69946.9167-5.170411.0068-0.1857-0.1107-0.15030.0409-0.0248-0.87030.53121.00480.21050.10770.0672-0.06160.1459-0.06340.23652.376876.779335.7836
273.45650.71781.4832.95732.46782.52040.0720.0569-0.45411.0044-0.3160.24980.7516-0.06230.24410.5525-0.18440.1440.21330.01140.33436.513671.786736.4734
282.5182-2.88440.00025.6450.47592.9912-0.15260.0561-0.39220.5043-0.10380.64130.3054-0.03590.25630.2146-0.14540.15150.1336-0.10650.209432.279566.116729.4186
294.4748-3.43470.12733.97430.13811.92640.01360.0095-0.53750.6747-0.18960.55190.47110.17620.1760.4328-0.08080.08850.126-0.05290.194840.964156.896826.4016
308.26962.3214-3.77220.6549-1.06811.7716-0.0469-0.1138-0.0574-0.0238-0.03-0.02590.01650.09520.07690.1302-0.07680.0360.1331-0.02080.186621.123770.400323.6642
310.54060.661-1.47828.40932.15976.60150.03030.0991-0.0413-0.04390.0192-0.65720.04690.1949-0.04960.05490.1360.09860.62670.04950.338729.948673.045475.6892
322.44130.29741.32195.38020.13942.18480.09060.2580.23890.4857-0.2369-1.10850.10880.42270.14620.06250.0063-0.080.40580.05290.279827.822174.754482.2803
336.84081.93190.20653.57333.71247.25160.13070.0231-0.33510.2512-0.2191-0.3115-0.08050.12660.08840.11940.0209-0.08870.20080.03460.087123.987662.77390.2871
342.14362.6156-1.57523.6261-1.49531.9378-0.1461-0.0998-0.5125-0.1349-0.2563-0.5230.36880.33410.40240.16470.21740.02040.4882-0.11310.202324.200759.30978.9319
358.7298-0.64592.72861.7315-2.74974.74550.05240.2574-0.133-0.1558-0.1264-0.03230.27760.19960.0740.1780.097-0.01340.1744-0.11560.101915.529353.583675.9939
360.4035-1.4366-0.0987.2803-0.91650.91280.08480.0667-0.1281-0.1602-0.30.07650.08720.1550.21520.26380.034-0.02770.3216-0.16680.191712.05559.586884.4829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 21
2X-RAY DIFFRACTION2A22 - 34
3X-RAY DIFFRACTION3A35 - 71
4X-RAY DIFFRACTION4A72 - 128
5X-RAY DIFFRACTION5A129 - 147
6X-RAY DIFFRACTION6A148 - 171
7X-RAY DIFFRACTION7B3 - 24
8X-RAY DIFFRACTION8B25 - 53
9X-RAY DIFFRACTION9B54 - 91
10X-RAY DIFFRACTION10B92 - 103
11X-RAY DIFFRACTION11B104 - 140
12X-RAY DIFFRACTION12B141 - 170
13X-RAY DIFFRACTION13C2 - 21
14X-RAY DIFFRACTION14C22 - 27
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