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Entry
Database: PDB / ID: 3mel
TitleCrystal Structure of Thiamin pyrophosphokinase family protein from Enterococcus faecalis, Northeast Structural Genomics Consortium Target EfR150
ComponentsThiamine diphosphokinase
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
: / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Rossmann fold ...: / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / Thiamine diphosphokinase / Thiamine diphosphokinase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.788 Å
AuthorsKuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. ...Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Snell, E.H. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target EfR150
Authors: Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Authors: Kuzin, A. / Abasidze, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Apr 8, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / 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_sites / atom_type / audit_author / cell / chem_comp / chem_comp_atom / chem_comp_bond / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.angle_alpha ..._atom_sites.fract_transf_matrix[1][3] / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _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 / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_entry_details.has_ligand_of_interest / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _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 / _pdbx_struct_sheet_hbond.sheet_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_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_method_to_determine_struct / _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.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_diffrn_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_sheet.id / _struct_sheet_order.sheet_id / _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 / _struct_sheet_range.sheet_id
Description: Ligand identity
Details: The metal in the original protein used to produce the crystal was experimentally determined and found to be different than that in the model.
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: Thiamine diphosphokinase
B: Thiamine diphosphokinase
C: Thiamine diphosphokinase
D: Thiamine diphosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,33818
Polymers96,5114
Non-polymers1,82714
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.286, 102.112, 94.277
Angle α, β, γ (deg.)90, 98.126, 90
Int Tables number4
Space group name H-MP1211
Detailsdimer,52.62 kD,96%

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thiamine diphosphokinase


Mass: 24127.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: thiN, DAI13_15455, NCTC13379_00805, P0083_14635, P0D81_02330, P0E79_12185
Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): + Magic
References: UniProt: A0A855UKG6, UniProt: Q82ZE3*PLUS, thiamine diphosphokinase

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: MgSO4 - 0.15M, Bis-Tris 0.1M, PEG8K 16%, ATP, MgCl2, thiamine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2010 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.788→50 Å / Num. obs: 56964 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 0 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDRickShaw serverphasing
RefinementMethod to determine structure: MAD
Starting model: GtR2

Resolution: 2.788→48.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.887 / SU B: 29.611 / SU ML: 0.269 / Cross valid method: FREE R-VALUE / ESU R Free: 0.356 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2493 1476 5.085 %
Rwork0.1679 27549 -
all0.172 --
obs-29025 99.17 %
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: 43.906 Å2
Baniso -1Baniso -2Baniso -3
1--1.942 Å2-0 Å2-1.008 Å2
2---1.031 Å20 Å2
3---3.134 Å2
Refinement stepCycle: LAST / Resolution: 2.788→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 100 67 6943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127038
X-RAY DIFFRACTIONr_angle_refined_deg2.7911.8229597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9485850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.604545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.498101095
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.72110345
X-RAY DIFFRACTIONr_chiral_restr0.1790.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025458
X-RAY DIFFRACTIONr_nbd_refined0.2570.23142
X-RAY DIFFRACTIONr_nbtor_refined0.3310.24607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2276
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.28
X-RAY DIFFRACTIONr_mcbond_it2.4532.1223409
X-RAY DIFFRACTIONr_mcangle_it3.9773.8064256
X-RAY DIFFRACTIONr_scbond_it3.9242.3363629
X-RAY DIFFRACTIONr_scangle_it6.0554.2035341
X-RAY DIFFRACTIONr_lrange_it7.76222.90910238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.788-2.860.3481080.27118770.27521500.9210.95692.32560.235
2.86-2.9390.3641060.27719770.28120980.9150.95299.2850.239
2.939-3.0230.3721230.2418820.24820140.9150.96499.55310.197
3.023-3.1160.2521010.20218820.20419940.9620.97599.44830.173
3.116-3.2180.291780.17718440.18219250.9460.9899.84420.152
3.218-3.330.2741020.18717350.19218400.9470.97899.8370.162
3.33-3.4550.252810.19417120.19717990.9510.97599.66650.171
3.455-3.5960.272760.18316230.18717020.9490.97899.82370.163
3.596-3.7550.198820.17616110.17716950.9750.97799.8820.156
3.755-3.9370.243700.15314840.15715620.9670.98599.48780.138
3.937-4.1480.204810.14214430.14515290.9670.98799.6730.126
4.148-4.3980.207740.13213320.13614080.9770.9999.8580.125
4.398-4.6990.247520.11212970.11613510.9620.99399.8520.109
4.699-5.0710.18710.11911860.12212580.9830.99299.92050.115
5.071-5.5490.252780.1510830.15711620.9660.98799.91390.144
5.549-6.1940.281500.16410000.16910500.9480.9871000.157
6.194-7.1330.318460.1738770.1799230.9620.9861000.167
7.133-8.6890.201490.1427560.1468050.980.9881000.148
8.689-12.0960.144340.125890.1226240.9850.99299.83970.133
12.096-48.530.311130.23590.2043720.9020.9741000.224
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2966-1.11640.94431.0022-0.32951.3587-0.0077-0.1430.1296-0.0119-0.0062-0.0375-0.0411-0.03470.01390.0164-0.00250.03940.09370.00310.111416.9905-5.186985.3254
20.5670.04151.22012.22320.62624.30120.0612-0.0776-0.06560.361-0.0328-0.10190.070.0392-0.02840.099-0.0176-0.00370.1004-0.00060.122923.0556-24.505298.9575
32.02080.25032.66391.48540.40774.3223-0.03680.07620.1291-0.1904-0.08710.1828-0.33210.03940.12390.3509-0.024-0.00070.1265-0.00360.1108-8.409712.284139.2143
40.88790.4229-0.30451.4872-0.80834.41610.05930.3099-0.24-0.3307-0.05180.01280.27030.0668-0.00750.20220.0593-0.01170.2281-0.03980.21950.1688-6.869951.5129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp2 - 904
2X-RAY DIFFRACTION2ALLBp2 - 229
3X-RAY DIFFRACTION3ALLCp2 - 229
4X-RAY DIFFRACTION4ALLDp2 - 904

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  • 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

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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

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