[English] 日本語
Yorodumi
- PDB-5agv: The sliding clamp of Mycobacterium tuberculosis in complex with a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5agv
TitleThe sliding clamp of Mycobacterium tuberculosis in complex with a natural product.
Components
  • CYCLOHEXYL GRISELIMYCIN
  • DNA POLYMERASE III SUBUNIT BETA
KeywordsTRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX / TRANSFERASE / DNAN / NATURAL PRODUCT / SLIDING CLAMP
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / peptidoglycan-based cell wall / DNA-directed DNA polymerase activity / response to antibiotic / DNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain ...DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / : / Roll / Alpha Beta
Similarity search - Domain/homology
: / (R,R)-2,3-BUTANEDIOL / : / Beta sliding clamp
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
STREPTOMYCES CAELICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLukat, P. / Kling, A. / Heinz, D.W. / Mueller, R.
CitationJournal: Science / Year: 2015
Title: Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins.
Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Konig, C. / Ammerman, N.C. / Barrio, M.B. / Borchers, K. / ...Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Konig, C. / Ammerman, N.C. / Barrio, M.B. / Borchers, K. / Bordon-Pallier, F. / Bronstrup, M. / Courtemanche, G. / Gerlitz, M. / Geslin, M. / Hammann, P. / Heinz, D.W. / Hoffmann, H. / Klieber, S. / Kohlmann, M. / Kurz, M. / Lair, C. / Matter, H. / Nuermberger, E. / Tyagi, S. / Fraisse, L. / Grosset, J.H. / Lagrange, S. / Muller, R.
History
DepositionFeb 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Derived calculations
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly_gen ...atom_site / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _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_atom_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_atom_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_atom_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 3.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 4.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_molecule_features / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.compound_details / _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_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_symmetry / _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.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.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 / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA POLYMERASE III SUBUNIT BETA
B: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32127
Polymers87,3544
Non-polymers96723
Water17,565975
1
B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules

A: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32127
Polymers87,3544
Non-polymers96723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area9250 Å2
ΔGint-192.3 kcal/mol
Surface area34420 Å2
MethodPISA
2
A: DNA POLYMERASE III SUBUNIT BETA
C: CYCLOHEXYL GRISELIMYCIN
hetero molecules

B: DNA POLYMERASE III SUBUNIT BETA
D: CYCLOHEXYL GRISELIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32127
Polymers87,3544
Non-polymers96723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area9250 Å2
ΔGint-192.3 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.869, 89.764, 81.928
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99984, 0.01309, 0.01194), (-0.01302, -0.9999, 0.00624), (0.01202, 0.00608, 0.99991)
Vector: -7.45966, 45.72646, 0.35453)

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein DNA POLYMERASE III SUBUNIT BETA


Mass: 42479.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
Plasmid: PVP008_DNANMTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6XU56, UniProt: P9WNU1*PLUS, DNA-directed DNA polymerase
#2: Protein/peptide CYCLOHEXYL GRISELIMYCIN


Type: Peptide-like / Class: Antibiotic / Mass: 1197.593 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES CAELICUS (bacteria) / References: BIRD: PRD_002466

-
Non-polymers , 4 types, 998 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsNovel synthetic analog of natural product Griselimycin
Nonpolymer detailsCYCLOHEXYLGRISELIMYCIN (CGM): CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF ...CYCLOHEXYLGRISELIMYCIN (CGM): CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF GRISELIMYCIN, A NATURAL PRODUCT SYNTHESIZED BY STREPTOMYCES CAELICUS.
Sequence detailsFIRST 4 N-TERMINAL RESIDUES ARE REMAINING FRIOM THE PROTEASE CLEAVAGE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growpH: 7.5
Details: 333 MM CACL2, 144 MM LITHIUM ACETATE, 11.7 % (W/V) PEG 8000, 100 MM HEPES-NAOH PH 7.58

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91844
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014 / Details: MIRRORS
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91844 Å / Relative weight: 1
ReflectionResolution: 1.93→40.8 Å / Num. obs: 79001 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 25.93 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.93→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERviaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WWPDB ENTRY 3P16

3p16


Resolution: 1.93→40.8 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
Details: WEAKLY DEFINED SIDECHAINS ARE MODELLED AS ALANINES.
RfactorNum. reflection% reflection
Rfree0.2095 3846 4.9 %
Rwork0.1688 --
obs0.1708 78969 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.47 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 48 975 6924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076428
X-RAY DIFFRACTIONf_angle_d1.1288866
X-RAY DIFFRACTIONf_dihedral_angle_d13.5172409
X-RAY DIFFRACTIONf_chiral_restr0.0461091
X-RAY DIFFRACTIONf_plane_restr0.0041177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9302-1.95460.27991240.23862805X-RAY DIFFRACTION100
1.9546-1.98040.27561590.24472735X-RAY DIFFRACTION100
1.9804-2.00750.33231360.23232783X-RAY DIFFRACTION100
2.0075-2.03620.26111270.2212796X-RAY DIFFRACTION100
2.0362-2.06660.2461350.20842755X-RAY DIFFRACTION100
2.0666-2.09890.22611430.20652794X-RAY DIFFRACTION100
2.0989-2.13330.24421300.20232770X-RAY DIFFRACTION100
2.1333-2.170.27411550.19982785X-RAY DIFFRACTION100
2.17-2.20950.2651520.19452759X-RAY DIFFRACTION100
2.2095-2.2520.22561490.18072753X-RAY DIFFRACTION100
2.252-2.2980.20681130.18182789X-RAY DIFFRACTION100
2.298-2.34790.21331400.18042793X-RAY DIFFRACTION100
2.3479-2.40250.21351460.1762750X-RAY DIFFRACTION100
2.4025-2.46260.21881550.17092756X-RAY DIFFRACTION100
2.4626-2.52920.24671530.17572766X-RAY DIFFRACTION100
2.5292-2.60360.2151440.17422803X-RAY DIFFRACTION100
2.6036-2.68760.21461370.17252761X-RAY DIFFRACTION100
2.6876-2.78370.25841270.17342777X-RAY DIFFRACTION100
2.7837-2.89510.2211610.17612797X-RAY DIFFRACTION100
2.8951-3.02680.22931440.16972774X-RAY DIFFRACTION100
3.0268-3.18630.21331430.16832768X-RAY DIFFRACTION100
3.1863-3.38590.18831340.16022797X-RAY DIFFRACTION100
3.3859-3.64710.20021500.15132791X-RAY DIFFRACTION100
3.6471-4.01390.17351560.14212785X-RAY DIFFRACTION100
4.0139-4.5940.1521330.13012816X-RAY DIFFRACTION100
4.594-5.78530.18881620.14362803X-RAY DIFFRACTION100
5.7853-40.80860.19251380.1782862X-RAY DIFFRACTION100
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)
10.4521-0.2425-0.02331.6549-1.24933.7114-0.0929-0.02310.03050.0105-0.1602-0.1685-0.14750.24860.2470.21790.0129-0.00610.21970.02650.302712.781524.207156.4395
21.7203-0.05740.09231.80861.28052.7459-0.0381-0.14630.1642-0.1357-0.02210.0076-0.4892-0.00220.0320.2517-0.0125-0.01630.15170.03120.217414.517127.454427.5305
30.93290.3665-0.33933.17010.57171.9820.05450.07110.061-0.2391-0.13870.0877-0.1244-0.13070.07380.15340.0142-0.00040.1948-0.00310.136110.42367.035810.885
40.13040.16570.3798-0.06540.0883.2804-0.0404-0.0255-0.01410.01260.00940.01480.3262-0.07110.03290.22980.0130.02610.18-0.00280.2419-19.694220.63945.4519
50.44480.119-0.43941.5392-1.17992.50320.0241-0.01370.0322-0.0333-0.0654-0.06560.00160.09080.05050.1233-0.0222-0.02090.1873-0.01640.1663-19.28834.163614.7637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 140 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 141 THROUGH 270 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 271 THROUGH 402 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 10 THROUGH 238 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 239 THROUGH 402 )

+
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