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Entry
Database: PDB / ID: 4ct3
TitleMethylmercury chloride derivative structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K
ComponentsORF30/ORF32
KeywordsVIRAL PROTEIN / PEPTIDOGLYCAN / PROTEASE
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / defense response to bacterium / proteolysis / metal ion binding
Similarity search - Function
Bacterial SH3 domain / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / CHAP domain profile. / CHAP domain / CHAP domain / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / METHYL MERCURY ION / Endolysin LysK
Similarity search - Component
Biological speciesKayvirus kay
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsSanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
Citation
Journal: Virol. J. / Year: 2014
Title: Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.
Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of the Chap Domain of the Endolysin from Staphylococcus Aureus Bacteriophage K.
Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
#2: Journal: Bacteriophage / Year: 2011
Title: In Silico Modeling of the Staphylococcal Bacteriophage-Derived Peptidase Chap(K).
Authors: Fenton, M. / Cooney, J.C. / Ross, R.P. / Sleator, R.D. / McAuliffe, O. / O'Mahony, J. / Coffey, A.
#3: Journal: Appl.Environ.Microbiol. / Year: 2009
Title: Phage Lysin Lysk Can be Truncated to its Chap Domain and Retain Lytic Activity Against Live Antibiotic-Resistant Staphylococci.
Authors: Horgan, M. / O'Flynn, G. / Garry, J. / Cooney, J. / Coffey, A. / Fitzgerald, G.F. / Ross, R.P. / McAuliffe, O.
History
DepositionMar 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jun 26, 2024Group: 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 / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _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_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_seq_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 / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_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_asym_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 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ORF30/ORF32
G: ORF30/ORF32
I: ORF30/ORF32
K: ORF30/ORF32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,59930
Polymers75,3024
Non-polymers4,29726
Water13,872770
1
E: ORF30/ORF32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0649
Polymers18,8251
Non-polymers1,2388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: ORF30/ORF32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9728
Polymers18,8251
Non-polymers1,1467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: ORF30/ORF32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7366
Polymers18,8251
Non-polymers9105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: ORF30/ORF32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8287
Polymers18,8251
Non-polymers1,0026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.020, 61.520, 72.800
Angle α, β, γ (deg.)91.80, 98.73, 90.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 165 / Label seq-ID: 2 - 165

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11EA
21GB
12EA
22IC
13EA
23KD
14GB
24IC
15GB
25KD
16IC
26KD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.99998, -0.00041, -0.00566), (-0.00041, 1, -0.00099), (0.00566, -0.00099, -0.99998)28.8107, 30.82522, 125.46037
2given(0.99959, -0.02871, 0.00018), (-0.02586, -0.89772, 0.43981), (-0.01247, -0.43963, -0.89809)-16.85748, -13.40129, 129.27524
3given(-0.99956, 0.02943, 0.00275), (-0.0252, -0.89706, 0.4412), (0.01545, 0.44093, 0.89741)6.12498, 17.25254, -3.83987
4given(-0.99956, -0.02914, 0.00561), (0.02371, -0.89798, -0.43939), (0.01784, -0.43907, 0.89828)12.14037, 68.70654, 29.59155
5given(0.99952, 0.02984, -0.00851), (0.02303, -0.89733, -0.44076), (-0.02079, 0.44035, -0.89759)-22.52818, 99.53175, 95.80234
6given(-0.99999, 0.00052, -0.00335), (0.00052, 1, -0.00161), (0.00335, -0.00161, -0.99999)-10.30666, 30.87002, 125.46338

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Components

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Protein , 1 types, 4 molecules EGIK

#1: Protein
ORF30/ORF32 / Putative endolysin


Mass: 18825.439 Da / Num. of mol.: 4 / Fragment: CHAPK, RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kayvirus kay / Gene: PhageK_071 / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q6Y7T6

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Non-polymers , 7 types, 796 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MMC / METHYL MERCURY ION


Mass: 215.625 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH3Hg
#7: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.5
Details: 25 MM TRIS-HCL, 22%(W/V) PEG 8000, 0.1 M 4-(2- HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID (HEPES)-NAOH PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8352
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013
Details: HORIZONTAL AND VERTICAL FOCUSSING MIRRORS AND SLITS
RadiationMonochromator: SI111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8352 Å / Relative weight: 1
ReflectionResolution: 1.69→71.92 Å / Num. obs: 48498 / % possible obs: 64.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.8 / % possible all: 10.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
xia2data reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.69→61.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.913 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22407 2431 5 %RANDOM
Rwork0.18074 ---
obs0.18291 46067 64.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20.09 Å20.84 Å2
2---1.47 Å20.22 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.69→61.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 132 770 6110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025488
X-RAY DIFFRACTIONr_bond_other_d0.0050.025079
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9397439
X-RAY DIFFRACTIONr_angle_other_deg1.032311711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026195
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021301
X-RAY DIFFRACTIONr_nbd_refined0.2540.21682
X-RAY DIFFRACTIONr_nbd_other0.1780.25107
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22693
X-RAY DIFFRACTIONr_nbtor_other0.0830.22574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.210
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.227
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2145
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.217
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4762.0192630
X-RAY DIFFRACTIONr_mcbond_other1.4772.0192629
X-RAY DIFFRACTIONr_mcangle_it2.4583.0213283
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8352.2252858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8993.2364151
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E100920.05
12G100920.05
21I100530.05
22K100530.05
31E100000.06
32K100000.06
41G100270.07
42I100270.07
51G99860.07
52K99860.07
61I100920.04
62K100920.04
LS refinement shellResolution: 1.69→1.781 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 62 -
Rwork0.279 1349 -
obs--12.92 %

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