[English] 日本語
Yorodumi
- PDB-7xxc: Orf1-glycine-glycylthricin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xxc
TitleOrf1-glycine-glycylthricin complex
ComponentsN-formimidoyl fortimicin A synthase
KeywordsOXIDOREDUCTASE / glycylthricin OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLYCINE / Chem-I55 / N-formimidoyl fortimicin A synthase
Similarity search - Component
Biological speciesStreptomyces luteocolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsWang, Y.L. / Li, T.L.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Other government Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Authors: Wang, Y.L. / Chang, C.Y. / Hsu, N.S. / Lo, I.W. / Lin, K.H. / Chen, C.L. / Chang, C.F. / Wang, Z.C. / Ogasawara, Y. / Dairi, T. / Maruyama, C. / Hamano, Y. / Li, T.L.
History
DepositionMay 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-formimidoyl fortimicin A synthase
B: N-formimidoyl fortimicin A synthase
C: N-formimidoyl fortimicin A synthase
D: N-formimidoyl fortimicin A synthase
E: N-formimidoyl fortimicin A synthase
F: N-formimidoyl fortimicin A synthase
G: N-formimidoyl fortimicin A synthase
H: N-formimidoyl fortimicin A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,75932
Polymers440,4238
Non-polymers10,33624
Water43,7042426
1
A: N-formimidoyl fortimicin A synthase
B: N-formimidoyl fortimicin A synthase
C: N-formimidoyl fortimicin A synthase
D: N-formimidoyl fortimicin A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,38016
Polymers220,2124
Non-polymers5,16812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-100 kcal/mol
Surface area64490 Å2
MethodPISA
2
E: N-formimidoyl fortimicin A synthase
F: N-formimidoyl fortimicin A synthase
G: N-formimidoyl fortimicin A synthase
H: N-formimidoyl fortimicin A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,38016
Polymers220,2124
Non-polymers5,16812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17660 Å2
ΔGint-100 kcal/mol
Surface area64660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.471, 108.062, 134.557
Angle α, β, γ (deg.)89.753, 90.080, 96.500
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158B
168C
179B
189D
1910B
2010E
2111B
2211F
2312B
2412G
2513B
2613H
2714C
2814D
2915C
3015E
3116C
3216F
3317C
3417G
3518C
3618H
3719D
3819E
3920D
4020F
4121D
4221G
4322D
4422H
4523E
4623F
4724E
4824G
4925E
5025H
5126F
5226G
5327F
5427H
5528G
5628H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTRPTRPAA11 - 49032 - 511
221THRTHRTRPTRPBB11 - 49032 - 511
332THRTHRTRPTRPAA11 - 49032 - 511
442THRTHRTRPTRPCC11 - 49032 - 511
553VALVALTRPTRPAA13 - 49034 - 511
663VALVALTRPTRPDD13 - 49034 - 511
774THRTHRTRPTRPAA11 - 49032 - 511
884THRTHRTRPTRPEE11 - 49032 - 511
995THRTHRTRPTRPAA11 - 49032 - 511
10105THRTHRTRPTRPFF11 - 49032 - 511
11116THRTHRHISHISAA11 - 49132 - 512
12126THRTHRHISHISGG11 - 49132 - 512
13137VALVALTRPTRPAA13 - 49034 - 511
14147VALVALTRPTRPHH13 - 49034 - 511
15158GLNGLNHISHISBB10 - 49131 - 512
16168GLNGLNHISHISCC10 - 49131 - 512
17179VALVALTRPTRPBB13 - 49034 - 511
18189VALVALTRPTRPDD13 - 49034 - 511
191910GLNGLNHISHISBB10 - 49131 - 512
202010GLNGLNHISHISEE10 - 49131 - 512
212111GLNGLNHISHISBB10 - 49131 - 512
222211GLNGLNHISHISFF10 - 49131 - 512
232312THRTHRTRPTRPBB11 - 49032 - 511
242412THRTHRTRPTRPGG11 - 49032 - 511
252513VALVALTRPTRPBB13 - 49034 - 511
262613VALVALTRPTRPHH13 - 49034 - 511
272714VALVALTRPTRPCC13 - 49034 - 511
282814VALVALTRPTRPDD13 - 49034 - 511
292915GLNGLNHISHISCC10 - 49131 - 512
303015GLNGLNHISHISEE10 - 49131 - 512
313116GLNGLNHISHISCC10 - 49131 - 512
323216GLNGLNHISHISFF10 - 49131 - 512
333317THRTHRTRPTRPCC11 - 49032 - 511
343417THRTHRTRPTRPGG11 - 49032 - 511
353518VALVALTRPTRPCC13 - 49034 - 511
363618VALVALTRPTRPHH13 - 49034 - 511
373719VALVALTRPTRPDD13 - 49034 - 511
383819VALVALTRPTRPEE13 - 49034 - 511
393920VALVALTRPTRPDD13 - 49034 - 511
404020VALVALTRPTRPFF13 - 49034 - 511
414121VALVALTRPTRPDD13 - 49034 - 511
424221VALVALTRPTRPGG13 - 49034 - 511
434322VALVALHISHISDD13 - 49134 - 512
444422VALVALHISHISHH13 - 49134 - 512
454523GLNGLNHISHISEE10 - 49131 - 512
464623GLNGLNHISHISFF10 - 49131 - 512
474724THRTHRTRPTRPEE11 - 49032 - 511
484824THRTHRTRPTRPGG11 - 49032 - 511
494925VALVALTRPTRPEE13 - 49034 - 511
505025VALVALTRPTRPHH13 - 49034 - 511
515126THRTHRTRPTRPFF11 - 49032 - 511
525226THRTHRTRPTRPGG11 - 49032 - 511
535327VALVALTRPTRPFF13 - 49034 - 511
545427VALVALTRPTRPHH13 - 49034 - 511
555528VALVALTRPTRPGG13 - 49034 - 511
565628VALVALTRPTRPHH13 - 49034 - 511

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

-
Components

#1: Protein
N-formimidoyl fortimicin A synthase


Mass: 55052.918 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces luteocolor (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125SZC1
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-I55 / [(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl] carbamate


Mass: 431.401 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H25N7O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.989→30 Å / Num. obs: 388255 / % possible obs: 97.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.018 / Rrim(I) all: 0.041 / Net I/σ(I): 38.1
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.26 / Num. unique obs: 37016 / Rpim(I) all: 0.127 / Rrim(I) all: 0.29 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XQA
Resolution: 1.989→27.822 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.332 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2209 18798 4.846 %
Rwork0.1979 369115 -
all0.199 --
obs-387913 97.476 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å20.009 Å20.013 Å2
2--0.134 Å2-0.106 Å2
3----0.055 Å2
Refinement stepCycle: LAST / Resolution: 1.989→27.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29166 0 704 2426 32296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01330648
X-RAY DIFFRACTIONr_bond_other_d0.0010.01728449
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.64241871
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57565313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61153854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11220.3041646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.746154557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.35715281
X-RAY DIFFRACTIONr_chiral_restr0.0690.23981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0235091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026951
X-RAY DIFFRACTIONr_nbd_refined0.1920.26012
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.226915
X-RAY DIFFRACTIONr_nbtor_refined0.1550.214693
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.213984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.22096
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.228
X-RAY DIFFRACTIONr_nbd_other0.2690.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.232
X-RAY DIFFRACTIONr_mcbond_it2.1012.96215443
X-RAY DIFFRACTIONr_mcbond_other2.12.96215441
X-RAY DIFFRACTIONr_mcangle_it3.1234.43219288
X-RAY DIFFRACTIONr_mcangle_other3.1234.43319288
X-RAY DIFFRACTIONr_scbond_it2.5583.25515205
X-RAY DIFFRACTIONr_scbond_other2.5583.25515205
X-RAY DIFFRACTIONr_scangle_it4.0414.76422583
X-RAY DIFFRACTIONr_scangle_other4.0414.76422583
X-RAY DIFFRACTIONr_lrange_it5.78335.00534250
X-RAY DIFFRACTIONr_lrange_other5.67934.78733775
X-RAY DIFFRACTIONr_ncsr_local_group_10.0470.0515233
X-RAY DIFFRACTIONr_ncsr_local_group_20.0530.0515155
X-RAY DIFFRACTIONr_ncsr_local_group_30.0520.0515085
X-RAY DIFFRACTIONr_ncsr_local_group_40.0270.0515471
X-RAY DIFFRACTIONr_ncsr_local_group_50.0450.0515248
X-RAY DIFFRACTIONr_ncsr_local_group_60.0540.0515175
X-RAY DIFFRACTIONr_ncsr_local_group_70.0510.0515092
X-RAY DIFFRACTIONr_ncsr_local_group_80.0590.0515285
X-RAY DIFFRACTIONr_ncsr_local_group_90.0520.0515127
X-RAY DIFFRACTIONr_ncsr_local_group_100.0480.0515359
X-RAY DIFFRACTIONr_ncsr_local_group_110.0310.0515597
X-RAY DIFFRACTIONr_ncsr_local_group_120.0490.0515197
X-RAY DIFFRACTIONr_ncsr_local_group_130.0520.0515147
X-RAY DIFFRACTIONr_ncsr_local_group_140.0530.0515146
X-RAY DIFFRACTIONr_ncsr_local_group_150.0550.0515272
X-RAY DIFFRACTIONr_ncsr_local_group_160.0510.0515334
X-RAY DIFFRACTIONr_ncsr_local_group_170.0320.0515477
X-RAY DIFFRACTIONr_ncsr_local_group_180.0510.0515139
X-RAY DIFFRACTIONr_ncsr_local_group_190.050.0515140
X-RAY DIFFRACTIONr_ncsr_local_group_200.0440.0515166
X-RAY DIFFRACTIONr_ncsr_local_group_210.050.0515110
X-RAY DIFFRACTIONr_ncsr_local_group_220.0170.0515467
X-RAY DIFFRACTIONr_ncsr_local_group_230.0460.0515320
X-RAY DIFFRACTIONr_ncsr_local_group_240.050.0515152
X-RAY DIFFRACTIONr_ncsr_local_group_250.0510.0515104
X-RAY DIFFRACTIONr_ncsr_local_group_260.0460.0515163
X-RAY DIFFRACTIONr_ncsr_local_group_270.0450.0515140
X-RAY DIFFRACTIONr_ncsr_local_group_280.0480.0515171
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.047450.05009
12BX-RAY DIFFRACTIONLocal ncs0.047450.05009
23AX-RAY DIFFRACTIONLocal ncs0.053220.05009
24CX-RAY DIFFRACTIONLocal ncs0.053220.05009
35AX-RAY DIFFRACTIONLocal ncs0.051990.05009
36DX-RAY DIFFRACTIONLocal ncs0.051990.05009
47AX-RAY DIFFRACTIONLocal ncs0.026530.0501
48EX-RAY DIFFRACTIONLocal ncs0.026530.0501
59AX-RAY DIFFRACTIONLocal ncs0.045480.05009
510FX-RAY DIFFRACTIONLocal ncs0.045480.05009
611AX-RAY DIFFRACTIONLocal ncs0.053960.05009
612GX-RAY DIFFRACTIONLocal ncs0.053960.05009
713AX-RAY DIFFRACTIONLocal ncs0.050970.05009
714HX-RAY DIFFRACTIONLocal ncs0.050970.05009
815BX-RAY DIFFRACTIONLocal ncs0.058510.05009
816CX-RAY DIFFRACTIONLocal ncs0.058510.05009
917BX-RAY DIFFRACTIONLocal ncs0.05230.05009
918DX-RAY DIFFRACTIONLocal ncs0.05230.05009
1019BX-RAY DIFFRACTIONLocal ncs0.048110.05009
1020EX-RAY DIFFRACTIONLocal ncs0.048110.05009
1121BX-RAY DIFFRACTIONLocal ncs0.031310.0501
1122FX-RAY DIFFRACTIONLocal ncs0.031310.0501
1223BX-RAY DIFFRACTIONLocal ncs0.049220.05009
1224GX-RAY DIFFRACTIONLocal ncs0.049220.05009
1325BX-RAY DIFFRACTIONLocal ncs0.05240.05009
1326HX-RAY DIFFRACTIONLocal ncs0.05240.05009
1427CX-RAY DIFFRACTIONLocal ncs0.052550.05009
1428DX-RAY DIFFRACTIONLocal ncs0.052550.05009
1529CX-RAY DIFFRACTIONLocal ncs0.054870.05009
1530EX-RAY DIFFRACTIONLocal ncs0.054870.05009
1631CX-RAY DIFFRACTIONLocal ncs0.050960.05009
1632FX-RAY DIFFRACTIONLocal ncs0.050960.05009
1733CX-RAY DIFFRACTIONLocal ncs0.032350.0501
1734GX-RAY DIFFRACTIONLocal ncs0.032350.0501
1835CX-RAY DIFFRACTIONLocal ncs0.050720.05009
1836HX-RAY DIFFRACTIONLocal ncs0.050720.05009
1937DX-RAY DIFFRACTIONLocal ncs0.050140.05009
1938EX-RAY DIFFRACTIONLocal ncs0.050140.05009
2039DX-RAY DIFFRACTIONLocal ncs0.043670.05009
2040FX-RAY DIFFRACTIONLocal ncs0.043670.05009
2141DX-RAY DIFFRACTIONLocal ncs0.049880.05009
2142GX-RAY DIFFRACTIONLocal ncs0.049880.05009
2243DX-RAY DIFFRACTIONLocal ncs0.017120.0501
2244HX-RAY DIFFRACTIONLocal ncs0.017120.0501
2345EX-RAY DIFFRACTIONLocal ncs0.045620.05009
2346FX-RAY DIFFRACTIONLocal ncs0.045620.05009
2447EX-RAY DIFFRACTIONLocal ncs0.049870.05009
2448GX-RAY DIFFRACTIONLocal ncs0.049870.05009
2549EX-RAY DIFFRACTIONLocal ncs0.050620.05009
2550HX-RAY DIFFRACTIONLocal ncs0.050620.05009
2651FX-RAY DIFFRACTIONLocal ncs0.046460.05009
2652GX-RAY DIFFRACTIONLocal ncs0.046460.05009
2753FX-RAY DIFFRACTIONLocal ncs0.04490.05009
2754HX-RAY DIFFRACTIONLocal ncs0.04490.05009
2855GX-RAY DIFFRACTIONLocal ncs0.048110.05009
2856HX-RAY DIFFRACTIONLocal ncs0.048110.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.989-2.040.27812620.25325814X-RAY DIFFRACTION92.356
2.04-2.0960.27213210.24226322X-RAY DIFFRACTION96.9148
2.096-2.1570.24913150.23225696X-RAY DIFFRACTION97.0188
2.157-2.2230.24512340.22224956X-RAY DIFFRACTION97.2305
2.223-2.2950.2412480.22124284X-RAY DIFFRACTION97.4058
2.295-2.3750.24211730.2123456X-RAY DIFFRACTION97.4981
2.375-2.4640.23711360.20622844X-RAY DIFFRACTION97.7379
2.464-2.5640.23211520.20521797X-RAY DIFFRACTION97.851
2.564-2.6770.25310910.21221012X-RAY DIFFRACTION98.0525
2.677-2.8070.23110240.20220150X-RAY DIFFRACTION98.1505
2.807-2.9570.22610290.20419181X-RAY DIFFRACTION98.3072
2.957-3.1350.2149390.19418237X-RAY DIFFRACTION98.5001
3.135-3.3480.2298090.20217156X-RAY DIFFRACTION98.6329
3.348-3.6130.2148000.19616035X-RAY DIFFRACTION98.8085
3.613-3.9520.2258030.18614658X-RAY DIFFRACTION98.9124
3.952-4.4090.1736530.1613389X-RAY DIFFRACTION98.9849
4.409-5.0730.1655970.15211830X-RAY DIFFRACTION99.0752
5.073-6.1690.25690.18310023X-RAY DIFFRACTION99.4741
6.169-8.5450.2034080.1817890X-RAY DIFFRACTION99.6158
8.545-27.8220.1992350.2024383X-RAY DIFFRACTION94.3604

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more