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- PDB-7xif: Crystal structure of the aminopropyltransferase, SpeE from hypert... -

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Basic information

Entry
Database: PDB / ID: 7xif
TitleCrystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) alone or together with spermidine or thermospermine
ComponentsPolyamine aminopropyltransferase
KeywordsTRANSFERASE / POLYAMINE BIOSYNTHESIS
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function
Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / SPERMIDINE / Chem-TER / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMizohata, E. / Yasuda, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17GB Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05780 Japan
New Energy and Industrial Technology Development Organization (NEDO)JPNP18016 Japan
CitationJournal: Catalysts / Year: 2022
Title: Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis.
Authors: Fukuda, W. / Osaki, M. / Yasuda, Y. / Hidese, R. / Higuchi, T. / Umezawa, N. / Fujiwara, S. / Mizohata, E.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
C: Polyamine aminopropyltransferase
D: Polyamine aminopropyltransferase
E: Polyamine aminopropyltransferase
F: Polyamine aminopropyltransferase
G: Polyamine aminopropyltransferase
H: Polyamine aminopropyltransferase
I: Polyamine aminopropyltransferase
J: Polyamine aminopropyltransferase
K: Polyamine aminopropyltransferase
L: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,21832
Polymers418,31712
Non-polymers4,90120
Water21,7261206
1
A: Polyamine aminopropyltransferase
F: Polyamine aminopropyltransferase
hetero molecules

C: Polyamine aminopropyltransferase
H: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,26612
Polymers139,4394
Non-polymers1,8278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
Buried area16080 Å2
ΔGint-48 kcal/mol
Surface area36690 Å2
MethodPISA
2
B: Polyamine aminopropyltransferase
D: Polyamine aminopropyltransferase
E: Polyamine aminopropyltransferase
hetero molecules

G: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,32412
Polymers139,4394
Non-polymers1,8858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x+y,-x,z-1/31
Buried area16410 Å2
ΔGint-52 kcal/mol
Surface area36550 Å2
MethodPISA
3
I: Polyamine aminopropyltransferase
L: Polyamine aminopropyltransferase
hetero molecules

K: Polyamine aminopropyltransferase
hetero molecules

J: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,6288
Polymers139,4394
Non-polymers1,1894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-y-1,x-y-1,z-2/31
crystal symmetry operation3_544-x+y,-x-1,z-1/31
Buried area14130 Å2
ΔGint-73 kcal/mol
Surface area37170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.159, 166.159, 149.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA4 - 28924 - 309
21ARGARGBB4 - 28924 - 309
12ARGARGAA4 - 28924 - 309
22ARGARGCC4 - 28924 - 309
13LEULEUAA4 - 28824 - 308
23LEULEUDD4 - 28824 - 308
14ARGARGAA4 - 28924 - 309
24ARGARGEE4 - 28924 - 309
15ARGARGAA4 - 28924 - 309
25ARGARGFF4 - 28924 - 309
16ARGARGAA4 - 28924 - 309
26ARGARGGG4 - 28924 - 309
17ARGARGAA4 - 28924 - 309
27ARGARGHH4 - 28924 - 309
18ARGARGAA4 - 28924 - 309
28ARGARGII4 - 28924 - 309
19ARGARGAA4 - 28924 - 309
29ARGARGJJ4 - 28924 - 309
110ARGARGAA4 - 28924 - 309
210ARGARGKK4 - 28924 - 309
111ARGARGAA4 - 28924 - 309
211ARGARGLL4 - 28924 - 309
112ARGARGBB4 - 28924 - 309
212ARGARGCC4 - 28924 - 309
113LEULEUBB4 - 28824 - 308
213LEULEUDD4 - 28824 - 308
114ARGARGBB4 - 28924 - 309
214ARGARGEE4 - 28924 - 309
115ARGARGBB4 - 28924 - 309
215ARGARGFF4 - 28924 - 309
116ARGARGBB4 - 28924 - 309
216ARGARGGG4 - 28924 - 309
117ARGARGBB4 - 28924 - 309
217ARGARGHH4 - 28924 - 309
118ARGARGBB4 - 28924 - 309
218ARGARGII4 - 28924 - 309
119ARGARGBB4 - 28924 - 309
219ARGARGJJ4 - 28924 - 309
120ARGARGBB4 - 28924 - 309
220ARGARGKK4 - 28924 - 309
121ARGARGBB4 - 28924 - 309
221ARGARGLL4 - 28924 - 309
122LEULEUCC4 - 28824 - 308
222LEULEUDD4 - 28824 - 308
123ARGARGCC4 - 28924 - 309
223ARGARGEE4 - 28924 - 309
124ARGARGCC4 - 28924 - 309
224ARGARGFF4 - 28924 - 309
125ARGARGCC4 - 28924 - 309
225ARGARGGG4 - 28924 - 309
126ARGARGCC4 - 28924 - 309
226ARGARGHH4 - 28924 - 309
127ARGARGCC4 - 28924 - 309
227ARGARGII4 - 28924 - 309
128ARGARGCC4 - 28924 - 309
228ARGARGJJ4 - 28924 - 309
129ARGARGCC4 - 28924 - 309
229ARGARGKK4 - 28924 - 309
130ARGARGCC4 - 28924 - 309
230ARGARGLL4 - 28924 - 309
131LEULEUDD4 - 28824 - 308
231LEULEUEE4 - 28824 - 308
132LEULEUDD4 - 28824 - 308
232LEULEUFF4 - 28824 - 308
133LEULEUDD4 - 28824 - 308
233LEULEUGG4 - 28824 - 308
134LEULEUDD4 - 28824 - 308
234LEULEUHH4 - 28824 - 308
135LEULEUDD4 - 28824 - 308
235LEULEUII4 - 28824 - 308
136LEULEUDD4 - 28824 - 308
236LEULEUJJ4 - 28824 - 308
137LEULEUDD4 - 28824 - 308
237LEULEUKK4 - 28824 - 308
138LEULEUDD4 - 28824 - 308
238LEULEULL4 - 28824 - 308
139ARGARGEE4 - 28924 - 309
239ARGARGFF4 - 28924 - 309
140ARGARGEE4 - 28924 - 309
240ARGARGGG4 - 28924 - 309
141ARGARGEE4 - 28924 - 309
241ARGARGHH4 - 28924 - 309
142ARGARGEE4 - 28924 - 309
242ARGARGII4 - 28924 - 309
143ARGARGEE4 - 28924 - 309
243ARGARGJJ4 - 28924 - 309
144ARGARGEE4 - 28924 - 309
244ARGARGKK4 - 28924 - 309
145ARGARGEE4 - 28924 - 309
245ARGARGLL4 - 28924 - 309
146ARGARGFF4 - 28924 - 309
246ARGARGGG4 - 28924 - 309
147ARGARGFF4 - 28924 - 309
247ARGARGHH4 - 28924 - 309
148ARGARGFF4 - 28924 - 309
248ARGARGII4 - 28924 - 309
149ARGARGFF4 - 28924 - 309
249ARGARGJJ4 - 28924 - 309
150ARGARGFF4 - 28924 - 309
250ARGARGKK4 - 28924 - 309
151ARGARGFF4 - 28924 - 309
251ARGARGLL4 - 28924 - 309
152ARGARGGG4 - 28924 - 309
252ARGARGHH4 - 28924 - 309
153ARGARGGG4 - 28924 - 309
253ARGARGII4 - 28924 - 309
154ARGARGGG4 - 28924 - 309
254ARGARGJJ4 - 28924 - 309
155ARGARGGG4 - 28924 - 309
255ARGARGKK4 - 28924 - 309
156ARGARGGG4 - 28924 - 309
256ARGARGLL4 - 28924 - 309
157ARGARGHH4 - 28924 - 309
257ARGARGII4 - 28924 - 309
158ARGARGHH4 - 28924 - 309
258ARGARGJJ4 - 28924 - 309
159ARGARGHH4 - 28924 - 309
259ARGARGKK4 - 28924 - 309
160ARGARGHH4 - 28924 - 309
260ARGARGLL4 - 28924 - 309
161ARGARGII4 - 28924 - 309
261ARGARGJJ4 - 28924 - 309
162ARGARGII4 - 28924 - 309
262ARGARGKK4 - 28924 - 309
163ARGARGII4 - 28924 - 309
263ARGARGLL4 - 28924 - 309
164ARGARGJJ4 - 28924 - 309
264ARGARGKK4 - 28924 - 309
165ARGARGJJ4 - 28924 - 309
265ARGARGLL4 - 28924 - 309
166ARGARGKK4 - 28924 - 309
266ARGARGLL4 - 28924 - 309

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

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Components

#1: Protein
Polyamine aminopropyltransferase / Putrescine aminopropyltransferase / PAPT / Spermidine synthase / SPDS / SPDSY


Mass: 34859.758 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: DSM 21063 / JCM 11548 / VA1 / Gene: speE, Pcal_0772 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MU81, spermidine synthase
#2: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TER / N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE / THERMOSPERMINE / PA(334)


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Sodium citrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.498
11K, H, -L20.502
ReflectionResolution: 2.14→47.97 Å / Num. obs: 254276 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 2.14→2.18 Å / Num. unique obs: 12626 / CC1/2: 0.526

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANX
Resolution: 2.14→47.11 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.959 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 12860 5.1 %RANDOM
Rwork0.16024 ---
obs0.16176 241370 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å20 Å20 Å2
2--3.11 Å20 Å2
3----6.22 Å2
Refinement stepCycle: 1 / Resolution: 2.14→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27332 0 332 1206 28870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01328388
X-RAY DIFFRACTIONr_bond_other_d0.0010.01527024
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.64638587
X-RAY DIFFRACTIONr_angle_other_deg1.3861.57962150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88653440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07621.6271524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.048154682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.00915208
X-RAY DIFFRACTIONr_chiral_restr0.0820.23695
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0231875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026417
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_it5.2864.5913751
X-RAY DIFFRACTIONr_mcbond_other5.2864.5913750
X-RAY DIFFRACTIONr_mcangle_it6.6786.87217176
X-RAY DIFFRACTIONr_mcangle_other6.6786.87217177
X-RAY DIFFRACTIONr_scbond_it6.2115.06114637
X-RAY DIFFRACTIONr_scbond_other6.2115.06114637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5527.38221406
X-RAY DIFFRACTIONr_long_range_B_refined10.44353.17130254
X-RAY DIFFRACTIONr_long_range_B_other10.44553.12530155
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)
11A95250.06
12B95250.06
21A94950.06
22C94950.06
31A94760.05
32D94760.05
41A95550.05
42E95550.05
51A94810.06
52F94810.06
61A95260.05
62G95260.05
71A94820.06
72H94820.06
81A94780.06
82I94780.06
91A93950.07
92J93950.07
101A95010.06
102K95010.06
111A94420.06
112L94420.06
121B95260.05
122C95260.05
131B94960.05
132D94960.05
141B95030.06
142E95030.06
151B94830.06
152F94830.06
161B94790.06
162G94790.06
171B94870.07
172H94870.07
181B94990.06
182I94990.06
191B94340.07
192J94340.07
201B94500.06
202K94500.06
211B94370.07
212L94370.07
221C95460.05
222D95460.05
231C95360.05
232E95360.05
241C95040.06
242F95040.06
251C94850.05
252G94850.05
261C94390.06
262H94390.06
271C95060.05
272I95060.05
281C94220.06
282J94220.06
291C94450.06
292K94450.06
301C94110.07
302L94110.07
311D95400.05
312E95400.05
321D95360.05
322F95360.05
331D94910.05
332G94910.05
341D94830.06
342H94830.06
351D95170.05
352I95170.05
361D94390.06
362J94390.06
371D94650.06
372K94650.06
381D94480.06
382L94480.06
391E95830.05
392F95830.05
401E96260.04
402G96260.04
411E95750.05
412H95750.05
421E95150.06
422I95150.06
431E94640.06
432J94640.06
441E94960.06
442K94960.06
451E94980.06
452L94980.06
461F95350.05
462G95350.05
471F95310.06
472H95310.06
481F95110.05
482I95110.05
491F94960.05
492J94960.05
501F94480.06
502K94480.06
511F94710.06
512L94710.06
521G95980.06
522H95980.06
531G95410.06
532I95410.06
541G95060.06
542J95060.06
551G95120.06
552K95120.06
561G95120.07
562L95120.07
571H95000.06
572I95000.06
581H94730.06
582J94730.06
591H94990.06
592K94990.06
601H95160.06
602L95160.06
611I94500.06
612J94500.06
621I94590.06
622K94590.06
631I94350.06
632L94350.06
641J93920.06
642K93920.06
651J94280.06
652L94280.06
661K94190.06
662L94190.06
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 981 -
Rwork0.462 17930 -
obs--99.78 %

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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

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