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- PDB-5vm5: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 5vm5
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser bound
ComponentsTryptophan synthase beta chain 1
KeywordsLYASE / PLP / non-canonical amino acid / directed evolution / allostery
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0JO / Chem-PLS / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsBuller, A.R. / van Roye, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM110851 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.
Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Structure summary
Category: entity / reflns / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _reflns.number_obs / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,04815
Polymers173,5624
Non-polymers1,48611
Water10,521584
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5237
Polymers86,7812
Non-polymers7415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-56 kcal/mol
Surface area25220 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5268
Polymers86,7812
Non-polymers7446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-49 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.123, 108.728, 160.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase beta chain 1


Mass: 43390.602 Da / Num. of mol.: 4
Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17N2O8P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.67→40 Å / Num. obs: 159409 / % possible obs: 99.7 % / Redundancy: 10 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Net I/σ(I): 10.7
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.638 / Rpim(I) all: 0.894 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.67→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.667 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22357 8361 5 %RANDOM
Rwork0.19566 ---
obs0.19705 159409 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.67→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11488 0 94 584 12166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911980
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211458
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.96916250
X-RAY DIFFRACTIONr_angle_other_deg0.914326281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58651568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65623.841492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.993151943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5181567
X-RAY DIFFRACTIONr_chiral_restr0.0770.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022705
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_it0.3210.7956191
X-RAY DIFFRACTIONr_mcbond_other0.320.7956190
X-RAY DIFFRACTIONr_mcangle_it0.5921.1897741
X-RAY DIFFRACTIONr_mcangle_other0.5921.1897742
X-RAY DIFFRACTIONr_scbond_it0.2670.8585789
X-RAY DIFFRACTIONr_scbond_other0.2670.8585790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5011.2698493
X-RAY DIFFRACTIONr_long_range_B_refined5.3117.17713619
X-RAY DIFFRACTIONr_long_range_B_other5.3117.17913620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 578 -
Rwork0.397 11533 -
obs--98.42 %
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)
10.4683-0.0453-0.41460.58250.31361.0908-0.0426-0.0504-0.05490.05890.0150.05050.1350.10980.02760.29490.01090.00460.25540.00770.0926.192-41.654-14.781
22.2465-0.1068-2.32451.09150.98594.5044-0.05050.15070.16810.0307-0.30540.2823-0.1502-0.73070.35590.2829-0.0063-0.02140.3156-0.12540.1575-12.656-45.233-15.981
33.05540.8756-0.46966.70622.41123.59080.0507-0.2409-0.10960.7782-0.23920.03990.7058-0.3160.18860.3941-0.05340.06190.21080.05590.078-2.333-53.878-5.232
40.4358-0.0488-0.36650.6572-0.03951.56120.0182-0.11390.06940.12760.04760.0065-0.13460.0384-0.06580.3298-0.00180.00990.2679-0.01740.08475.439-30.32-7.706
53.8150.6784-9.90943.7089-4.380431.29940.06780.07430.0647-0.00280.28780.27490.8431-0.8478-0.35560.5043-0.11560.02410.35740.02910.2247-13.834-34.5483.887
60.67650.0622-0.28780.59880.04772.08270.0757-0.0280.1160.05080.0140.0948-0.2246-0.2106-0.08970.3140.03610.03670.2318-0.01230.0758-2.552-23.989-13.065
73.30941.5490.36193.0534-0.11982.35720.1045-0.0780.2124-0.0909-0.10010.2251-0.2485-0.3025-0.00440.34090.05950.0360.2824-0.02340.1259-1.008-23.692-20.907
80.23860.36580.30812.0020.8861.7965-0.01970.09530.0164-0.35970.08650.1066-0.2326-0.0436-0.06680.42960.02530.01430.25080.04090.02753.938-25.874-62.436
90.59970.2332-0.06921.33220.27671.3855-0.02520.01470.0196-0.08640.0458-0.0749-0.07980.0587-0.02060.3041-0.01940.00460.2722-0.0010.09210.102-36.667-37.415
102.2820.1566-0.65531.7690.89383.09640.0221-0.0499-0.10230.0424-0.12980.12850.1004-0.26760.10770.33620.02190.00160.24040.00230.0915-4.966-25.15-42.931
110.7597-0.4888-0.00030.99350.35931.16280.04780.0574-0.0104-0.1917-0.08570.1363-0.1793-0.28910.03790.3509-0.0003-0.00990.2404-0.00290.0411-2.266-28.395-48.371
121.0965-0.05040.19090.86050.01861.0836-0.02850.092-0.0582-0.17980.01930.0110.1182-0.08660.00920.386-0.034-0.00320.2603-0.01760.07073.882-45.506-52.451
130.77060.0632-0.47690.9686-0.0122.4478-0.00870.1254-0.0476-0.1536-0.01140.16330.0592-0.31110.02020.3334-0.0396-0.03560.2536-0.02270.0859-2.691-47.608-47.557
143.0188-0.6883-0.57612.11220.18282.0578-0.02680.0081-0.17580.0454-0.03550.11160.2024-0.24390.06240.3463-0.0625-0.01950.2678-0.00760.10021.264-51.271-38.576
151.333-0.70890.277111.19050.33271.482-0.3127-0.59240.13330.47510.31290.0845-0.2235-0.0285-0.00020.33370.0467-0.02240.3493-0.06280.100133.017-13.197-15.151
163.72921.48133.76622.25952.36278.4355-0.0233-0.20280.07590.0430.07130.0426-0.1127-0.4302-0.04790.28830.0530.00070.2512-0.00630.147221.454-8.678-29.987
170.5739-0.00830.21270.7742-0.5441.3-0.0340.03150.07070.0023-0.0089-0.1079-0.0407-0.05590.04290.3218-0.0182-0.01790.24470.01170.10735.922-15.967-41.455
181.2424-0.8960.7032.6638-0.85472.8817-0.24270.00330.16020.448-0.2611-0.3647-0.38830.56530.50380.4229-0.1057-0.12590.23160.09160.116447.241-4.512-31.938
190.673-0.0742-0.14260.55550.16811.5685-0.0563-0.12620.01280.10030.028-0.07250.06120.04530.02830.354-0.0058-0.03140.24640.01760.083336.862-23.257-28.624
201.0536-0.0609-0.47990.7205-0.21912.4801-0.0013-0.0873-0.04260.01950.0067-0.14470.14550.2527-0.00540.33330.0203-0.04260.21730.01840.091446.149-28.051-33.468
211.54730.0317-0.00121.85290.27112.61210.0850.0394-0.02150.0809-0.1005-0.13280.12020.27980.01550.36040.0428-0.03370.28810.01040.115644.786-29.898-41.951
220.29910.4341-0.22962.4395-0.49493.1272-0.07540.0374-0.053-0.285-0.0128-0.16360.41710.10340.08820.43630.00460.02070.2471-0.01390.016342.833-26.542-83.796
232.77830.64930.53773.58223.582810.7879-0.06210.3155-0.3484-0.18110.1181-0.07240.6099-0.3013-0.0560.348-0.06650.0090.24240.01760.143732.03-34.081-64.441
240.7619-0.25670.06460.773-0.21931.3638-0.01560.0757-0.0047-0.01270.0249-0.05490.1630.0905-0.00930.3459-0.031-0.00790.24850.00570.073340.009-19.283-60.352
251.9437-0.34510.95112.6901-0.41412.392-0.02660.40680.1888-0.1674-0.2839-0.2738-0.01960.78450.31050.2547-0.01080.00440.40520.09740.063356.898-20.423-66.105
260.4831-0.1052-0.17060.78820.03571.3638-0.01540.09230.0372-0.12070.046-0.01120.0319-0.0299-0.03060.3428-0.038-0.00950.27580.01840.04636.658-13.119-72.285
271.4420.45840.55041.17440.63882.6124-0.01310.24550.0261-0.18170.1081-0.1609-0.13760.2909-0.0950.3354-0.04610.02370.24710.04090.046344.057-5.04-73.185
281.3495-0.0606-0.25411.4709-0.09172.22990.030.04380.20820.07490.0209-0.0499-0.22170.0474-0.05080.3649-0.0396-0.0080.23310.02390.108538.162-2.481-58.314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 132
2X-RAY DIFFRACTION2A133 - 164
3X-RAY DIFFRACTION3A165 - 182
4X-RAY DIFFRACTION4A183 - 282
5X-RAY DIFFRACTION5A283 - 292
6X-RAY DIFFRACTION6A293 - 358
7X-RAY DIFFRACTION7A359 - 384
8X-RAY DIFFRACTION8B1 - 27
9X-RAY DIFFRACTION9B28 - 84
10X-RAY DIFFRACTION10B85 - 141
11X-RAY DIFFRACTION11B142 - 212
12X-RAY DIFFRACTION12B213 - 281
13X-RAY DIFFRACTION13B282 - 352
14X-RAY DIFFRACTION14B353 - 385
15X-RAY DIFFRACTION15C1 - 15
16X-RAY DIFFRACTION16C16 - 38
17X-RAY DIFFRACTION17C39 - 132
18X-RAY DIFFRACTION18C133 - 176
19X-RAY DIFFRACTION19C177 - 288
20X-RAY DIFFRACTION20C289 - 357
21X-RAY DIFFRACTION21C358 - 383
22X-RAY DIFFRACTION22D1 - 27
23X-RAY DIFFRACTION23D28 - 45
24X-RAY DIFFRACTION24D46 - 130
25X-RAY DIFFRACTION25D131 - 177
26X-RAY DIFFRACTION26D178 - 280
27X-RAY DIFFRACTION27D281 - 332
28X-RAY DIFFRACTION28D333 - 385

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