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- PDB-9hu9: Glycosyltransferase C from the Limosilactobacillus reuteri access... -

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Basic information

Entry
Database: PDB / ID: 9hu9
TitleGlycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Complex with UDP-GlcNAc.
ComponentsGlucosyltransferase 3
KeywordsTRANSFERASE / glycosyl transferase / GT113
Function / homologyGlucosyltransferase 3 / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / : / nucleotide binding / CITRIC ACID / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / URIDINE-5'-DIPHOSPHATE / Glucosyltransferase 3
Function and homology information
Biological speciesLimosilactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPfalzgraf, H.E. / Griffiths, R. / Juge, N. / Hemmings, A.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A structural basis for the strain-dependent UDP-sugar specificity of glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system.
Authors: Griffiths, R. / Pfalzgraf, H. / Latousakis, D. / Ashworth, G. / Dong, C. / Hemmings, A. / Juge, N.
History
DepositionDec 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 2.0Dec 10, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / chem_comp_atom / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_database_related / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / symmetry
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Atomic clashes
Details: Re-refinement of atomic model following reviewers' requests.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosyltransferase 3
B: Glucosyltransferase 3
C: Glucosyltransferase 3
D: Glucosyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,44014
Polymers153,7414
Non-polymers2,69910
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-58 kcal/mol
Surface area49190 Å2
Unit cell
Length a, b, c (Å)76.639, 121.392, 174.099
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

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

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUAA1 - 3333 - 335
211LEULEUBB1 - 3333 - 335
322LEULEUAA1 - 3333 - 335
422LEULEUCC1 - 3333 - 335
533LEULEUAA1 - 3333 - 335
633LEULEUDD1 - 3333 - 335
744HISHISBB0 - 3332 - 335
844HISHISCC0 - 3332 - 335
955HISHISBB0 - 3342 - 336
1055HISHISDD0 - 3342 - 336
1166HISHISCC0 - 3332 - 335
1266HISHISDD0 - 3332 - 335

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

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucosyltransferase 3


Mass: 38435.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus (bacteria) / Gene: gtf3, gtfC, Lreu23DRAFT_5181 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3XPQ7, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 7 types, 202 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: ammonium hydrogen citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→60.7 Å / Num. obs: 64276 / % possible obs: 99.68 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.52 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.099 / Net I/σ(I): 5.62
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 0.58 / Num. unique obs: 6327 / CC1/2: 0.516 / Rpim(I) all: 0.9018

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→60.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 28.159 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / ESU R: 0.385 / ESU R Free: 0.242
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2312 3212 5.002 %
Rwork0.1892 61008 -
all0.191 --
obs-64220 99.904 %
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: 48.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.744 Å2-0 Å20 Å2
2--1.358 Å2-0 Å2
3----0.613 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10844 0 172 192 11208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01211323
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610364
X-RAY DIFFRACTIONr_angle_refined_deg2.4691.78715451
X-RAY DIFFRACTIONr_angle_other_deg0.8331.74423803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83551338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.136540
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg4.69954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.569101785
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.12610572
X-RAY DIFFRACTIONr_chiral_restr0.1220.21691
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022709
X-RAY DIFFRACTIONr_nbd_refined0.2290.22281
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.29555
X-RAY DIFFRACTIONr_nbtor_refined0.20.25651
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.26511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.224
X-RAY DIFFRACTIONr_nbd_other0.2340.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.26
X-RAY DIFFRACTIONr_mcbond_it2.6832.0325361
X-RAY DIFFRACTIONr_mcbond_other2.6812.0325361
X-RAY DIFFRACTIONr_mcangle_it4.1383.6396696
X-RAY DIFFRACTIONr_mcangle_other4.1383.6396697
X-RAY DIFFRACTIONr_scbond_it5.0862.6465962
X-RAY DIFFRACTIONr_scbond_other5.072.6435959
X-RAY DIFFRACTIONr_scangle_it7.4364.6378755
X-RAY DIFFRACTIONr_scangle_other7.4364.6388756
X-RAY DIFFRACTIONr_lrange_it8.70121.84212589
X-RAY DIFFRACTIONr_lrange_other8.721.84612590
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.0510571
X-RAY DIFFRACTIONr_ncsr_local_group_20.1080.0510679
X-RAY DIFFRACTIONr_ncsr_local_group_30.1160.0510490
X-RAY DIFFRACTIONr_ncsr_local_group_40.1010.0510755
X-RAY DIFFRACTIONr_ncsr_local_group_50.1160.0510526
X-RAY DIFFRACTIONr_ncsr_local_group_60.1110.0510531
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.115010.05008
12BX-RAY DIFFRACTIONLocal ncs0.115010.05008
23AX-RAY DIFFRACTIONLocal ncs0.108330.05008
24CX-RAY DIFFRACTIONLocal ncs0.108330.05008
35AX-RAY DIFFRACTIONLocal ncs0.116290.05008
36DX-RAY DIFFRACTIONLocal ncs0.116290.05008
47BX-RAY DIFFRACTIONLocal ncs0.101020.05008
48CX-RAY DIFFRACTIONLocal ncs0.101020.05008
59BX-RAY DIFFRACTIONLocal ncs0.115740.05008
510DX-RAY DIFFRACTIONLocal ncs0.115740.05008
611CX-RAY DIFFRACTIONLocal ncs0.111010.05008
612DX-RAY DIFFRACTIONLocal ncs0.111010.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3632030.3424462X-RAY DIFFRACTION99.8288
2.462-2.530.3192370.3194327X-RAY DIFFRACTION99.8032
2.53-2.6030.3112170.3114217X-RAY DIFFRACTION99.9549
2.603-2.6830.3142190.3074102X-RAY DIFFRACTION99.8844
2.683-2.7710.3292200.2833963X-RAY DIFFRACTION99.8091
2.771-2.8680.292150.2493827X-RAY DIFFRACTION99.9011
2.868-2.9760.2681890.2233755X-RAY DIFFRACTION99.9493
2.976-3.0970.2551750.2053583X-RAY DIFFRACTION99.9202
3.097-3.2340.2471890.1953439X-RAY DIFFRACTION99.9449
3.234-3.3910.2371750.1843314X-RAY DIFFRACTION99.9427
3.391-3.5740.2341920.1883124X-RAY DIFFRACTION99.8795
3.574-3.790.2181680.1682979X-RAY DIFFRACTION99.9048
3.79-4.0510.1861340.1432836X-RAY DIFFRACTION99.9327
4.051-4.3740.1811340.1332605X-RAY DIFFRACTION99.8906
4.374-4.7890.1731360.1152445X-RAY DIFFRACTION100
4.789-5.350.1691200.1232197X-RAY DIFFRACTION100
5.35-6.170.2131010.1581969X-RAY DIFFRACTION100
6.17-7.5370.242890.1641702X-RAY DIFFRACTION100
7.537-100.17610.1311340X-RAY DIFFRACTION100
8-100.255380.247822X-RAY DIFFRACTION100
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)
12.3018-1.2972-1.1373.36531.4082.30690.17210.19130.0328-0.1255-0.1071-0.0774-0.19070.0285-0.0650.1918-0.0386-0.01880.06750.01880.2639.75427.253414.6868
22.31420.2625-0.75841.9018-0.11452.0386-0.0044-0.0451-0.0186-0.1226-0.0120.0909-0.0849-0.11610.01640.1527-0.0061-0.04950.0118-0.00180.284816.518136.150133.9426
33.7671-0.51070.32422.0625-0.01891.42470.00840.0488-0.2791-0.049-0.023-0.06340.091-0.01850.01460.1612-0.02650.02090.03640.01650.31884.7142-2.662932.143
44.23990.30430.41232.1762-0.51411.33030.0415-0.1983-0.19720.0114-0.01060.13150.05180.1206-0.03080.17320.03270.01410.06320.01150.311135.5798-9.095732.0415
52.13830.83661.25681.0521.34894.57560.00560.5135-0.0519-0.29930.0573-0.0797-0.3535-0.1396-0.06290.26270.06060.02430.2402-0.00240.412231.77767.7154-2.0147
61.5897-0.66011.52461.2666-1.28173.3559-0.0701-0.31710.04780.32060.12030.0938-0.1055-0.09-0.05020.2730.00860.05470.17820.01080.399817.021823.223257.1128
71.6066-0.17261.5550.4899-0.76844.62290.1240.1345-0.1279-0.0666-0.0502-0.03650.2684-0.0346-0.07390.16060.01290.03590.1021-0.00190.3903-2.633711.731110.9816
80.84030.03660.4761.79441.73663.5342-0.0374-0.15210.00340.15790.0707-0.1609-0.03370.1376-0.03330.1927-0.0033-0.00480.11940.00870.363149.81899.346646.4382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp2 - 155
2X-RAY DIFFRACTION2ALLBp2 - 155
3X-RAY DIFFRACTION3ALLCp2 - 155
4X-RAY DIFFRACTION4ALLDp2 - 155
5X-RAY DIFFRACTION5ALLAp156 - 334
6X-RAY DIFFRACTION6ALLBp156 - 334
7X-RAY DIFFRACTION7ALLCp156 - 334
8X-RAY DIFFRACTION8ALLDp156 - 334

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