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- PDB-2jbl: PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS -

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Basic information

Entry
Database: PDB / ID: 2jbl
TitlePHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS
Components
  • (REACTION CENTER PROTEIN ...Photosynthetic reaction centre) x 3
  • PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
KeywordsELECTRON TRANSPORT / CHROMOPHORE / FORMYLATION / CHLOROPHYLL / LIPOPROTEIN / STIGMATELLIN / METAL-BINDING / TRANSMEMBRANE / IRON / HEME / MEMBRANE / TRANSPORT / MAGNESIUM / PHOTOSYNTHESIS / REACTION CENTER / BACTERIOCHLOROPHYLL / PHOTOSYNTHETIC REACTION CENTER
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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 ...Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Multiheme cytochrome c family profile. / 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 centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / HEME C / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / STIGMATELLIN A / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBLASTOCHLORIS VIRIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLancaster, C.R.D.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex.
Authors: Lancaster, C.R.D. / Hunte, C. / Kelley, J. / Trumpower, B.L. / Ditchfield, R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Structural Basis of the Drastically Increased Initial Electron Transfer Rate in the Reaction Center from a Rhodopseudomonas Viridis Mutant Described at 2.00-A Resolution
Authors: Lancaster, C.R.D. / Bibikova, M. / Sabatino, P. / Oesterhelt, D. / Michel, H.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid
Authors: Lancaster, C.R. / Michel, H.
#3: Journal: Biochim.Biophys.Acta / Year: 1998
Title: Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications
Authors: Lancaster, C.R.D.
#4: Journal: Structure / Year: 1997
Title: The Coupling of Light-Induced Electron Transfer and Proton Uptake as Derived from Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb
Authors: Lancaster, C.R. / Michel, H.
#5: Journal: J.Mol.Biol. / Year: 1995
Title: Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Epp, O. / Sinning, I. / Michel, H.
#6: Journal: Science / Year: 1989
Title: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Michel, H.
#7: Journal: Nature / Year: 1985
Title: Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H.
#8: Journal: J.Mol.Biol. / Year: 1984
Title: X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H.
#9: Journal: J.Mol.Biol. / Year: 1982
Title: Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
Authors: Michel, H.
History
DepositionDec 8, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionMar 13, 2007ID: 4PRC
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms ...diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Sep 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / 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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
H: REACTION CENTER PROTEIN H CHAIN
L: REACTION CENTER PROTEIN L CHAIN
M: REACTION CENTER PROTEIN M CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,78528
Polymers134,3784
Non-polymers11,40724
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)223.500, 223.500, 113.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules C

#1: Protein PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT / SUBUNIT C / CYTOCHROME C558/C559


Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P07173

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REACTION CENTER PROTEIN ... , 3 types, 3 molecules HLM

#2: Protein REACTION CENTER PROTEIN H CHAIN / Photosynthetic reaction centre / SUBUNIT H / PHOTOSYNTHETIC REACTION CENTER H SUBUNIT


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06008
#3: Protein REACTION CENTER PROTEIN L CHAIN / Photosynthetic reaction centre / SUBUNIT L / PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06009
#4: Protein REACTION CENTER PROTEIN M CHAIN / Photosynthetic reaction centre / SUBUNIT M / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06010

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Non-polymers , 10 types, 366 molecules

#5: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#9: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#10: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O7
#11: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#12: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#13: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.28 %
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 13, 1992 / Details: FOCUSING MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→26.56 Å / Num. obs: 103499 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.6 / % possible all: 86.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PRC

4prc
PDB Unreleased entry


Resolution: 2.4→26.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3307055.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1500 1.4 %SHELLS
Rwork0.19 ---
obs0.19 103499 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1587 Å2 / ksol: 0.285982 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→26.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9342 0 808 342 10492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 231 1.4 %
Rwork0.259 15741 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARHCSDX_IUB.RCVTOPHCSDX_IUB.RCV
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5S07_PAR.TXTS07_TOP.TXT

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