[English] 日本語
Yorodumi
- PDB-2hg9: Reaction centre from Rhodobacter sphaeroides strain R-26.1 comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hg9
TitleReaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with tetrabrominated phosphatidylcholine
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS/MEMBRANE PROTEIN / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / LIPID BINDING SITES / BROMINATED LIPIDS / MEMBRANE PROTEIN / PHOTOSYNTHESIS-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / : / Chem-PC7 / Chem-PCK / PHOSPHATE ION / UBIQUINONE-10 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / : / Chem-PC7 / Chem-PCK / PHOSPHATE ION / UBIQUINONE-10 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRoszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J.
CitationJournal: Biochemistry / Year: 2007
Title: Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides.
Authors: Roszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.4Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Reaction center protein H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,00035
Polymers93,8113
Non-polymers13,18932
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40890 Å2
ΔGint-271 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.554, 139.554, 184.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Reaction center protein ... , 3 types, 3 molecules LMH

#1: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y8
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y9
#3: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid.
Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26.1 / References: UniProt: P0C0Y7

-
Non-polymers , 13 types, 473 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#7: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#9: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#11: Chemical ChemComp-PCK / (7R,18S,19R)-18,19-DIBROMO-7-{[(9S,10S)-9,10-DIBROMOOCTADECANOYL]OXY}-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-P HOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE / TETRABROMINATED PHOSPHATIDYLCHOLINE / 1,2-DISTEAROYL(9,10-DIBROMO)-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 1106.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85Br4NO8P
#12: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#13: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#14: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#15: Chemical ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC


Mass: 763.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Potassium phosphate, LDAO, 1,2,3-heptanetriol, dioxane, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2004 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.45→39.37 Å / Num. obs: 76588 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.8 / Num. unique all: 11112 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished structure of reaction centre at 1.95A resolution

Resolution: 2.45→39.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.135 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors; all details in the pdb-file
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.198 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the above average isotropic B value is an average residual B after TLS refinement while the final average atomic B is 55.5
RfactorNum. reflection% reflectionSelection details
Rfree0.20914 3709 4.9 %RANDOM
Rwork0.1788 ---
all0.18035 75227 --
obs0.18035 71518 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 853 441 7769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227653
X-RAY DIFFRACTIONr_bond_other_d0.0010.025263
X-RAY DIFFRACTIONr_angle_refined_deg1.7382.05510424
X-RAY DIFFRACTIONr_angle_other_deg1.2443.00312601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20822.664289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.632151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811533
X-RAY DIFFRACTIONr_chiral_restr0.1050.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021563
X-RAY DIFFRACTIONr_nbd_refined0.2210.21686
X-RAY DIFFRACTIONr_nbd_other0.2010.25321
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23618
X-RAY DIFFRACTIONr_nbtor_other0.0920.23448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.216
X-RAY DIFFRACTIONr_mcbond_it0.7511.54085
X-RAY DIFFRACTIONr_mcbond_other0.1951.51689
X-RAY DIFFRACTIONr_mcangle_it1.35326542
X-RAY DIFFRACTIONr_scbond_it2.3333623
X-RAY DIFFRACTIONr_scangle_it3.3074.53877
X-RAY DIFFRACTIONCruickshank estimated coordinate error0.198
X-RAY DIFFRACTIONMaximum Likelihood estimated coordinate error0.115
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 271 -
Rwork0.224 5233 -
obs-5233 98.15 %
Refinement TLS params.Method: refined / Origin x: 56.0554 Å / Origin y: 60.6887 Å / Origin z: 65.0923 Å
111213212223313233
T-0.2879 Å20.0768 Å20.0402 Å2--0.0106 Å20.0144 Å2---0.1762 Å2
L1.4063 °20.5871 °2-0.5787 °2-1.2054 °2-0.4162 °2--1.0894 °2
S-0.0257 Å °0.0716 Å °0.0363 Å °-0.0842 Å °0.0688 Å °-0.0411 Å °-0.0683 Å °-0.0911 Å °-0.0431 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION1M1 - 301
3X-RAY DIFFRACTION1H11 - 251
4X-RAY DIFFRACTION1M311 - 313
5X-RAY DIFFRACTION1L312 - 314
6X-RAY DIFFRACTION1M401
7X-RAY DIFFRACTION1L402
8X-RAY DIFFRACTION1M500
9X-RAY DIFFRACTION1M501
10X-RAY DIFFRACTION1L502
11X-RAY DIFFRACTION1H700 - 709
12X-RAY DIFFRACTION1M701 - 711
13X-RAY DIFFRACTION1L703 - 712
14X-RAY DIFFRACTION1H801
15X-RAY DIFFRACTION1M800 - 802
16X-RAY DIFFRACTION1H901 - 908
17X-RAY DIFFRACTION1M902 - 920
18X-RAY DIFFRACTION1H1001 - 1441
19X-RAY DIFFRACTION1M1004 - 1440
20X-RAY DIFFRACTION1L1002 - 1428

+
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