[English] 日本語
Yorodumi
- PDB-7ywu: Eugenol oxidase from rhodococcus jostii: mutant S81H, A423M, H434... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ywu
TitleEugenol oxidase from rhodococcus jostii: mutant S81H, A423M, H434Y, S394V, I445D, S518P
ComponentsProbable vanillyl-alcohol oxidase
KeywordsOXIDOREDUCTASE / biocatalysis / thermostability / oxidase / flavoenzyme
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / FAD binding
Similarity search - Function
Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
2-methoxy-4-(prop-2-en-1-yl)phenol / FLAVIN-ADENINE DINUCLEOTIDE / HEXANE-1,6-DIOL / Chem-I7I / Probable vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlvigini, L. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)H2020-837890European Union
CitationJournal: Nat Commun / Year: 2022
Title: Structure- and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound.
Authors: Guo, Y. / Alvigini, L. / Trajkovic, M. / Alonso-Cotchico, L. / Monza, E. / Savino, S. / Maric, I. / Mattevi, A. / Fraaije, M.W.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable vanillyl-alcohol oxidase
B: Probable vanillyl-alcohol oxidase
C: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
E: Probable vanillyl-alcohol oxidase
F: Probable vanillyl-alcohol oxidase
G: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,28427
Polymers471,1898
Non-polymers8,09519
Water59433
1
A: Probable vanillyl-alcohol oxidase
D: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,14310
Polymers117,7972
Non-polymers2,3468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable vanillyl-alcohol oxidase
C: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9097
Polymers117,7972
Non-polymers2,1125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Probable vanillyl-alcohol oxidase
G: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6976
Polymers117,7972
Non-polymers1,9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Probable vanillyl-alcohol oxidase
H: Probable vanillyl-alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5354
Polymers117,7972
Non-polymers1,7372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.641, 79.429, 189.180
Angle α, β, γ (deg.)90.000, 96.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA2 - 5262 - 526
21LEULEUBB2 - 5262 - 526
12ARGARGAA2 - 5222 - 522
22ARGARGCC2 - 5222 - 522
13LEULEUAA2 - 5262 - 526
23LEULEUDD2 - 5262 - 526
14PHEPHEAA2 - 5212 - 521
24PHEPHEEE2 - 5212 - 521
15GLNGLNAA2 - 5242 - 524
25GLNGLNFF2 - 5242 - 524
16ARGARGAA2 - 5222 - 522
26ARGARGGG2 - 5222 - 522
17PHEPHEAA2 - 5212 - 521
27PHEPHEHH2 - 5212 - 521
18ARGARGBB2 - 5222 - 522
28ARGARGCC2 - 5222 - 522
19LEULEUBB2 - 5262 - 526
29LEULEUDD2 - 5262 - 526
110PHEPHEBB2 - 5212 - 521
210PHEPHEEE2 - 5212 - 521
111GLNGLNBB2 - 5242 - 524
211GLNGLNFF2 - 5242 - 524
112ARGARGBB2 - 5222 - 522
212ARGARGGG2 - 5222 - 522
113PHEPHEBB2 - 5212 - 521
213PHEPHEHH2 - 5212 - 521
114ARGARGCC2 - 5222 - 522
214ARGARGDD2 - 5222 - 522
115PHEPHECC2 - 5212 - 521
215PHEPHEEE2 - 5212 - 521
116ARGARGCC2 - 5222 - 522
216ARGARGFF2 - 5222 - 522
117GLYGLYCC2 - 5232 - 523
217GLYGLYGG2 - 5232 - 523
118PHEPHECC2 - 5212 - 521
218PHEPHEHH2 - 5212 - 521
119PHEPHEDD2 - 5212 - 521
219PHEPHEEE2 - 5212 - 521
120GLNGLNDD2 - 5242 - 524
220GLNGLNFF2 - 5242 - 524
121ARGARGDD2 - 5222 - 522
221ARGARGGG2 - 5222 - 522
122PHEPHEDD2 - 5212 - 521
222PHEPHEHH2 - 5212 - 521
123PHEPHEEE2 - 5212 - 521
223PHEPHEFF2 - 5212 - 521
124PHEPHEEE2 - 5212 - 521
224PHEPHEGG2 - 5212 - 521
125PHEPHEEE2 - 5212 - 521
225PHEPHEHH2 - 5212 - 521
126ARGARGFF2 - 5222 - 522
226ARGARGGG2 - 5222 - 522
127PHEPHEFF2 - 5212 - 521
227PHEPHEHH2 - 5212 - 521
128PHEPHEGG2 - 5212 - 521
228PHEPHEHH2 - 5212 - 521

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.059525, -0.368574, 0.92769), (-0.206398, -0.9138, -0.349812), (0.976656, -0.170651, -0.130468)-57.627979, 27.18976, -22.557159
3given(1), (1), (1)
4given(-0.097944, -0.006987, -0.995167), (0.005556, -0.999964, 0.006474), (-0.995176, -0.004895, 0.09798)99.672546, -10.73132, 54.889648
5given(1), (1), (1)
6given(-0.925951, 0.376054, 0.034605), (0.375934, 0.909175, 0.179094), (0.035887, 0.178842, -0.983223)36.850159, -10.0761, 29.752581
7given(1), (1), (1)
8given(0.225342, 0.798863, -0.557709), (-0.751343, -0.221931, -0.621475), (-0.620246, 0.559075, 0.550209)39.356659, 98.370499, 69.276932
9given(1), (1), (1)
10given(-0.739119, -0.64354, 0.198895), (-0.607334, 0.509021, -0.609954), (0.291288, -0.571624, -0.76707)11.89151, 37.56039, 82.689201
11given(1), (1), (1)
12given(-0.502184, -0.806014, 0.313292), (-0.716104, 0.184512, -0.673165), (0.484775, -0.562402, -0.669849)38.372551, 106.931183, -19.550119
13given(1), (1), (1)
14given(0.481398, 0.758451, -0.439326), (-0.774862, 0.133977, -0.617769), (-0.409688, 0.63781, 0.652191)42.97459, 43.158138, -44.524368
15given(1), (1), (1)
16given(-0.9789, 0.201303, 0.035104), (0.200932, 0.917016, 0.34454), (0.037166, 0.344324, -0.938115)92.832687, -36.57917, 149.079926
17given(1), (1), (1)
18given(-0.097815, 0.00944, -0.99516), (-0.008223, -0.999929, -0.008677), (-0.995171, 0.007335, 0.097886)64.406609, -9.70099, 93.856758
19given(1), (1), (1)
20given(-0.437165, 0.639531, 0.632366), (0.709096, -0.187416, 0.679749), (0.553236, 0.74557, -0.371557)80.771629, -116.455437, 53.041458
21given(1), (1), (1)
22given(0.365851, -0.701644, -0.611432), (0.77781, -0.130239, 0.614857), (-0.511043, -0.700524, 0.498097)104.788773, -53.055099, 47.132488
23given(1), (1), (1)
24given(0.591024, -0.635567, -0.496735), (0.757135, 0.22465, 0.613416), (-0.278275, -0.738639, 0.613983)-7.77872, -108.77948, 60.733768
25given(1), (1), (1)
26given(-0.211347, 0.640894, 0.737962), (0.60026, -0.510754, 0.615482), (0.771375, 0.57305, -0.276757)-18.739679, -47.950291, 90.644257
27given(1), (1), (1)
28given(0.057201, -0.209944, 0.976039), (-0.369961, -0.912494, -0.174594), (0.927285, -0.351109, -0.129867)31.166451, -0.08415, 60.067009
29given(1), (1), (1)
30given(0.591099, -0.635748, -0.496415), (0.75274, 0.213664, 0.62268), (-0.289802, -0.741736, 0.604849)-7.80725, -108.741753, 62.13324
31given(1), (1), (1)
32given(-0.220546, 0.634784, 0.740546), (0.610907, -0.501974, 0.612221), (0.760363, 0.587428, -0.277085)-18.808331, -47.80201, 90.395653
33given(1), (1), (1)
34given(-0.437011, 0.639732, 0.63227), (0.717321, -0.176214, 0.674091), (0.542652, 0.748126, -0.381886)80.716614, -116.87532, 54.468731
35given(1), (1), (1)
36given(0.356194, -0.708619, -0.609085), (0.773522, -0.142068, 0.61764), (-0.524203, -0.691141, 0.497529)104.764931, -53.008732, 46.994061
37given(1), (1), (1)
38given(-0.513475, -0.803076, 0.302346), (-0.709093, 0.198674, -0.676547), (0.48325, -0.561781, -0.671469)39.880581, 106.599312, -19.37219
39given(1), (1), (1)
40given(0.466376, 0.766738, -0.441141), (-0.778135, 0.118414, -0.616834), (-0.420713, 0.630944, 0.651851)42.92244, 43.385818, -44.382599
41given(1), (1), (1)
42given(0.212721, 0.795525, -0.567353), (-0.753209, -0.236374, -0.613843), (-0.622435, 0.557913, 0.548915)40.859348, 98.12114, 69.501312
43given(1), (1), (1)
44given(-0.751913, -0.62887, 0.197865), (-0.596605, 0.521372, -0.610109), (0.280518, -0.576796, -0.767213)11.67414, 37.40028, 82.783546
45given(1), (1), (1)
46given(0.108791, -0.17299, 0.978897), (-0.292717, -0.946656, -0.13476), (0.94999, -0.271879, -0.153625)31.177481, -0.93687, 60.467781
47given(1), (1), (1)
48given(0.124154, 0.028692, 0.991848), (0.028481, -0.999273, 0.025341), (0.991854, 0.025102, -0.124881)48.446621, -52.326191, -53.654579
49given(1), (1), (1)
50given(0.944625, -0.325817, -0.039063), (0.327914, 0.93271, 0.150084), (-0.012466, -0.154582, 0.987901)112.869133, -48.42281, -30.336571
51given(1), (1), (1)
52given(0.947168, 0.320224, -0.018165), (-0.318868, 0.934026, -0.160993), (-0.034587, 0.15828, 0.986788)-91.45137, 76.75148, 41.341221
53given(1), (1), (1)
54given(-0.005, -0.45622, 0.889853), (-0.469713, -0.784515, -0.404853), (0.882805, -0.42, -0.21037)-63.427639, 55.597778, 100.325218
55given(1), (1), (1)
56given(0.114467, -0.167398, 0.979222), (-0.300693, -0.945301, -0.126449), (0.946827, -0.279971, -0.158541)31.24349, -1.45241, 61.096142

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Probable vanillyl-alcohol oxidase


Mass: 58898.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro03282 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q0SBK1, vanillyl-alcohol oxidase

-
Non-polymers , 6 types, 52 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EOL / 2-methoxy-4-(prop-2-en-1-yl)phenol / eugenol / Eugenol


Mass: 164.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H12O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-I7I / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(1~{R})-1-(3-methoxy-4-oxidanyl-phenyl)propyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate


Mass: 951.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H47N9O17P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl 2 , 0.1 M Tris pH 8.5, 3.4 M 1,6-Hexandiol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.8→49.58 Å / Num. obs: 106726 / % possible obs: 97.8 % / Redundancy: 3.5 % / CC1/2: 0.974 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.103 / Rrim(I) all: 0.195 / Net I/σ(I): 6.6 / Num. measured all: 377956 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.853.71.0991.353260.4680.6671.28998.8
15.34-49.583.20.0556890.8570.0410.06894.7

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FXD

5fxd


Resolution: 2.8→49.34 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 22.795 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 5453 5.1 %RANDOM
Rwork0.2274 ---
obs0.2299 101258 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.52 Å2 / Biso mean: 51.175 Å2 / Biso min: 5.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å22.49 Å2
2---0.33 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2.8→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32647 0 552 33 33232
Biso mean--48 24.11 -
Num. residues----4186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01334115
X-RAY DIFFRACTIONr_bond_other_d0.0020.01730611
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.64846413
X-RAY DIFFRACTIONr_angle_other_deg1.291.57670978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64954178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17222.4771813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.398155265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.73915211
X-RAY DIFFRACTIONr_chiral_restr0.0620.24222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0238649
X-RAY DIFFRACTIONr_gen_planes_other0.0040.027280
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4060TIGHT POSITIONAL0.270.13
1A4049TIGHT POSITIONAL0.280.13
1A4015TIGHT POSITIONAL0.270.13
1A3987TIGHT POSITIONAL0.290.13
1A4089TIGHT POSITIONAL0.240.13
1A4051TIGHT POSITIONAL0.250.13
1A4031TIGHT POSITIONAL0.270.13
1A4024TIGHT POSITIONAL0.260.13
1A3988TIGHT POSITIONAL0.280.13
1A4060TIGHT POSITIONAL0.270.13
1A4113TIGHT THERMAL6.931.32
2A4053TIGHT POSITIONAL0.280.13
2A4023TIGHT POSITIONAL0.280.13
2A3987TIGHT POSITIONAL0.290.13
2A4010TIGHT POSITIONAL0.310.13
2A3991TIGHT POSITIONAL0.270.13
2A3974TIGHT POSITIONAL0.290.13
2A3969TIGHT POSITIONAL0.270.13
2A3945TIGHT POSITIONAL0.280.13
2A3950TIGHT POSITIONAL0.30.13
2A4086TIGHT THERMAL3.581.32
3A4125TIGHT THERMAL4.781.32
4A4057TIGHT THERMAL12.951.32
5A4053TIGHT THERMAL14.971.32
6A4020TIGHT THERMAL16.771.32
7A3984TIGHT THERMAL19.131.32
8B4081TIGHT THERMAL6.41.32
9B4116TIGHT THERMAL4.171.32
10B4060TIGHT THERMAL10.991.32
11B4049TIGHT THERMAL10.691.32
12B4015TIGHT THERMAL12.851.32
13B3987TIGHT THERMAL15.161.32
14C4089TIGHT THERMAL5.191.32
15C4051TIGHT THERMAL11.181.32
16C4031TIGHT THERMAL12.921.32
17C4024TIGHT THERMAL14.881.32
18C3988TIGHT THERMAL16.871.32
19D4060TIGHT THERMAL12.461.32
20D4053TIGHT THERMAL13.221.32
21D4023TIGHT THERMAL15.261.32
22D3987TIGHT THERMAL17.641.32
23E4010TIGHT THERMAL9.431.32
24E3991TIGHT THERMAL7.961.32
25E3974TIGHT THERMAL11.091.32
26F3969TIGHT THERMAL7.941.32
27F3945TIGHT THERMAL6.951.32
28G3950TIGHT THERMAL8.241.32
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 409 -
Rwork0.346 7572 -
all-7981 -
obs--98.58 %

+
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