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- PDB-7xxm: Orf1-glycine-4-aminobutylthricin complex -

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Basic information

Entry
Database: PDB / ID: 7xxm
TitleOrf1-glycine-4-aminobutylthricin complex
ComponentsN-formimidoyl fortimicin A synthase
KeywordsOXIDOREDUCTASE / 4-aminobutylthricin 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-I60 / N-formimidoyl fortimicin A synthase
Similarity search - Component
Biological speciesStreptomyces luteocolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.119 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 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)450,98432
Polymers440,4238
Non-polymers10,56124
Water43,6682424
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)225,49216
Polymers220,2124
Non-polymers5,28012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
ΔGint-100 kcal/mol
Surface area64220 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)225,49216
Polymers220,2124
Non-polymers5,28012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-99 kcal/mol
Surface area64250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.644, 107.875, 134.782
Angle α, β, γ (deg.)89.963, 90.132, 83.438
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:

End auth comp-ID: HIS / End label comp-ID: HIS

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNAA10 - 49131 - 512
221GLNGLNBB10 - 49131 - 512
332GLNGLNAA10 - 49131 - 512
442GLNGLNCC10 - 49131 - 512
553ILEILEAA14 - 49135 - 512
663ILEILEDD14 - 49135 - 512
774GLNGLNAA10 - 49131 - 512
884GLNGLNEE10 - 49131 - 512
995GLNGLNAA10 - 49131 - 512
10105GLNGLNFF10 - 49131 - 512
11116GLNGLNAA10 - 49131 - 512
12126GLNGLNGG10 - 49131 - 512
13137VALVALAA13 - 49134 - 512
14147VALVALHH13 - 49134 - 512
15158GLNGLNBB10 - 49131 - 512
16168GLNGLNCC10 - 49131 - 512
17179ILEILEBB14 - 49135 - 512
18189ILEILEDD14 - 49135 - 512
191910GLNGLNBB10 - 49131 - 512
202010GLNGLNEE10 - 49131 - 512
212111GLNGLNBB10 - 49131 - 512
222211GLNGLNFF10 - 49131 - 512
232312GLNGLNBB10 - 49131 - 512
242412GLNGLNGG10 - 49131 - 512
252513VALVALBB13 - 49134 - 512
262613VALVALHH13 - 49134 - 512
272714ILEILECC14 - 49135 - 512
282814ILEILEDD14 - 49135 - 512
292915GLNGLNCC10 - 49131 - 512
303015GLNGLNEE10 - 49131 - 512
313116GLNGLNCC10 - 49131 - 512
323216GLNGLNFF10 - 49131 - 512
333317GLNGLNCC10 - 49131 - 512
343417GLNGLNGG10 - 49131 - 512
353518VALVALCC13 - 49134 - 512
363618VALVALHH13 - 49134 - 512
373719ILEILEDD14 - 49135 - 512
383819ILEILEEE14 - 49135 - 512
393920ILEILEDD14 - 49135 - 512
404020ILEILEFF14 - 49135 - 512
414121ILEILEDD14 - 49135 - 512
424221ILEILEGG14 - 49135 - 512
434322ILEILEDD14 - 49135 - 512
444422ILEILEHH14 - 49135 - 512
454523GLNGLNEE10 - 49131 - 512
464623GLNGLNFF10 - 49131 - 512
474724GLNGLNEE10 - 49131 - 512
484824GLNGLNGG10 - 49131 - 512
494925VALVALEE13 - 49134 - 512
505025VALVALHH13 - 49134 - 512
515126GLNGLNFF10 - 49131 - 512
525226GLNGLNGG10 - 49131 - 512
535327VALVALFF13 - 49134 - 512
545427VALVALHH13 - 49134 - 512
555528VALVALGG13 - 49134 - 512
565628VALVALHH13 - 49134 - 512

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

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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


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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-I60 / [(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-(4-azanylbutanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl] carbamate


Mass: 459.454 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H29N7O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2424 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
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

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.119→30 Å / Num. obs: 322706 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.025 / Rrim(I) all: 0.053 / Net I/σ(I): 30
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 31907 / Rpim(I) all: 0.32 / Rrim(I) all: 0.68 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XQA
Resolution: 2.119→29.393 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.189 / SU B: 4.338 / SU ML: 0.111 / Average fsc free: 0.9197 / Average fsc work: 0.9264 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2148 16133 5.06 %
Rwork0.1946 302700 -
all0.196 --
obs-318833 96.761 %
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: 31.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.129 Å20.032 Å2-0.005 Å2
2--0.112 Å20.082 Å2
3---0.022 Å2
Refinement stepCycle: LAST / Resolution: 2.119→29.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28839 0 720 2424 31983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01330300
X-RAY DIFFRACTIONr_bond_other_d0.0020.01728137
X-RAY DIFFRACTIONr_angle_refined_deg1.411.64141386
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57564610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81353801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.40420.3831618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58154502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.40915272
X-RAY DIFFRACTIONr_chiral_restr0.0670.23940
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0234616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026840
X-RAY DIFFRACTIONr_nbd_refined0.1910.26125
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.226335
X-RAY DIFFRACTIONr_nbtor_refined0.1550.214648
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.213512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.22139
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.230
X-RAY DIFFRACTIONr_nbd_other0.2460.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.220
X-RAY DIFFRACTIONr_mcbond_it2.1853.09415252
X-RAY DIFFRACTIONr_mcbond_other2.1843.09415250
X-RAY DIFFRACTIONr_mcangle_it3.3394.62719037
X-RAY DIFFRACTIONr_mcangle_other3.3384.62719037
X-RAY DIFFRACTIONr_scbond_it2.8383.47915048
X-RAY DIFFRACTIONr_scbond_other2.8383.47915049
X-RAY DIFFRACTIONr_scangle_it4.4885.09922349
X-RAY DIFFRACTIONr_scangle_other4.4885.122350
X-RAY DIFFRACTIONr_lrange_it6.66837.42634173
X-RAY DIFFRACTIONr_lrange_other6.66837.42734174
X-RAY DIFFRACTIONr_ncsr_local_group_10.0490.0515294
X-RAY DIFFRACTIONr_ncsr_local_group_20.0620.0514714
X-RAY DIFFRACTIONr_ncsr_local_group_30.0520.0514695
X-RAY DIFFRACTIONr_ncsr_local_group_40.0150.0515581
X-RAY DIFFRACTIONr_ncsr_local_group_50.0480.0515296
X-RAY DIFFRACTIONr_ncsr_local_group_60.0650.0514675
X-RAY DIFFRACTIONr_ncsr_local_group_70.050.0514679
X-RAY DIFFRACTIONr_ncsr_local_group_80.060.0514806
X-RAY DIFFRACTIONr_ncsr_local_group_90.0510.0514734
X-RAY DIFFRACTIONr_ncsr_local_group_100.0490.0515352
X-RAY DIFFRACTIONr_ncsr_local_group_110.010.0515630
X-RAY DIFFRACTIONr_ncsr_local_group_120.0620.0514766
X-RAY DIFFRACTIONr_ncsr_local_group_130.0490.0514727
X-RAY DIFFRACTIONr_ncsr_local_group_140.0620.0514265
X-RAY DIFFRACTIONr_ncsr_local_group_150.0620.0514761
X-RAY DIFFRACTIONr_ncsr_local_group_160.060.0514815
X-RAY DIFFRACTIONr_ncsr_local_group_170.0270.0515218
X-RAY DIFFRACTIONr_ncsr_local_group_180.0720.0514128
X-RAY DIFFRACTIONr_ncsr_local_group_190.0510.0514737
X-RAY DIFFRACTIONr_ncsr_local_group_200.0510.0514743
X-RAY DIFFRACTIONr_ncsr_local_group_210.0640.0514240
X-RAY DIFFRACTIONr_ncsr_local_group_220.020.0514837
X-RAY DIFFRACTIONr_ncsr_local_group_230.0480.0515314
X-RAY DIFFRACTIONr_ncsr_local_group_240.0640.0514686
X-RAY DIFFRACTIONr_ncsr_local_group_250.0490.0514685
X-RAY DIFFRACTIONr_ncsr_local_group_260.0620.0514774
X-RAY DIFFRACTIONr_ncsr_local_group_270.0490.0514724
X-RAY DIFFRACTIONr_ncsr_local_group_280.0730.0514105
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.048670.05009
12BX-RAY DIFFRACTIONLocal ncs0.048670.05009
23AX-RAY DIFFRACTIONLocal ncs0.062070.05009
24CX-RAY DIFFRACTIONLocal ncs0.062070.05009
35AX-RAY DIFFRACTIONLocal ncs0.052470.05009
36DX-RAY DIFFRACTIONLocal ncs0.052470.05009
47AX-RAY DIFFRACTIONLocal ncs0.014960.0501
48EX-RAY DIFFRACTIONLocal ncs0.014960.0501
59AX-RAY DIFFRACTIONLocal ncs0.047970.05009
510FX-RAY DIFFRACTIONLocal ncs0.047970.05009
611AX-RAY DIFFRACTIONLocal ncs0.064760.05008
612GX-RAY DIFFRACTIONLocal ncs0.064760.05008
713AX-RAY DIFFRACTIONLocal ncs0.050180.05009
714HX-RAY DIFFRACTIONLocal ncs0.050180.05009
815BX-RAY DIFFRACTIONLocal ncs0.05960.05008
816CX-RAY DIFFRACTIONLocal ncs0.05960.05008
917BX-RAY DIFFRACTIONLocal ncs0.050590.05009
918DX-RAY DIFFRACTIONLocal ncs0.050590.05009
1019BX-RAY DIFFRACTIONLocal ncs0.048540.05009
1020EX-RAY DIFFRACTIONLocal ncs0.048540.05009
1121BX-RAY DIFFRACTIONLocal ncs0.009730.0501
1122FX-RAY DIFFRACTIONLocal ncs0.009730.0501
1223BX-RAY DIFFRACTIONLocal ncs0.061960.05008
1224GX-RAY DIFFRACTIONLocal ncs0.061960.05008
1325BX-RAY DIFFRACTIONLocal ncs0.049170.05009
1326HX-RAY DIFFRACTIONLocal ncs0.049170.05009
1427CX-RAY DIFFRACTIONLocal ncs0.062160.05009
1428DX-RAY DIFFRACTIONLocal ncs0.062160.05009
1529CX-RAY DIFFRACTIONLocal ncs0.061820.05009
1530EX-RAY DIFFRACTIONLocal ncs0.061820.05009
1631CX-RAY DIFFRACTIONLocal ncs0.060380.05009
1632FX-RAY DIFFRACTIONLocal ncs0.060380.05009
1733CX-RAY DIFFRACTIONLocal ncs0.026960.0501
1734GX-RAY DIFFRACTIONLocal ncs0.026960.0501
1835CX-RAY DIFFRACTIONLocal ncs0.071540.05009
1836HX-RAY DIFFRACTIONLocal ncs0.071540.05009
1937DX-RAY DIFFRACTIONLocal ncs0.050970.05009
1938EX-RAY DIFFRACTIONLocal ncs0.050970.05009
2039DX-RAY DIFFRACTIONLocal ncs0.05110.05009
2040FX-RAY DIFFRACTIONLocal ncs0.05110.05009
2141DX-RAY DIFFRACTIONLocal ncs0.064310.05009
2142GX-RAY DIFFRACTIONLocal ncs0.064310.05009
2243DX-RAY DIFFRACTIONLocal ncs0.019670.0501
2244HX-RAY DIFFRACTIONLocal ncs0.019670.0501
2345EX-RAY DIFFRACTIONLocal ncs0.04790.05009
2346FX-RAY DIFFRACTIONLocal ncs0.04790.05009
2447EX-RAY DIFFRACTIONLocal ncs0.064440.05008
2448GX-RAY DIFFRACTIONLocal ncs0.064440.05008
2549EX-RAY DIFFRACTIONLocal ncs0.048670.05009
2550HX-RAY DIFFRACTIONLocal ncs0.048670.05009
2651FX-RAY DIFFRACTIONLocal ncs0.062290.05009
2652GX-RAY DIFFRACTIONLocal ncs0.062290.05009
2753FX-RAY DIFFRACTIONLocal ncs0.048540.05009
2754HX-RAY DIFFRACTIONLocal ncs0.048540.05009
2855GX-RAY DIFFRACTIONLocal ncs0.073120.05009
2856HX-RAY DIFFRACTIONLocal ncs0.073120.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.119-2.1740.2829910.27118399X-RAY DIFFRACTION79.7253
2.174-2.2340.27211080.25621665X-RAY DIFFRACTION95.6768
2.234-2.2990.26410780.24321444X-RAY DIFFRACTION97.4219
2.299-2.3690.24711400.22420727X-RAY DIFFRACTION97.5683
2.369-2.4470.24710960.21320171X-RAY DIFFRACTION97.7478
2.447-2.5330.24110310.20919547X-RAY DIFFRACTION97.8786
2.533-2.6280.24410380.20818899X-RAY DIFFRACTION98.0235
2.628-2.7360.2369350.20218213X-RAY DIFFRACTION98.1194
2.736-2.8570.2439320.217440X-RAY DIFFRACTION98.3038
2.857-2.9970.2099800.19816646X-RAY DIFFRACTION98.4363
2.997-3.1590.2198450.19415981X-RAY DIFFRACTION98.6053
3.159-3.350.2187920.19715122X-RAY DIFFRACTION98.7466
3.35-3.5810.217360.19314218X-RAY DIFFRACTION98.8563
3.581-3.8680.1976820.18213247X-RAY DIFFRACTION99.026
3.868-4.2370.1855710.16512262X-RAY DIFFRACTION99.1654
4.237-4.7360.1686600.15110997X-RAY DIFFRACTION99.293
4.736-5.4680.1784930.1619788X-RAY DIFFRACTION99.4968
5.468-6.6940.2144930.1918186X-RAY DIFFRACTION99.5984
6.694-9.4550.1583610.1596371X-RAY DIFFRACTION99.7777
9.455-29.3930.1821710.1843377X-RAY DIFFRACTION96.0476

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  • 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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