[English] 日本語
Yorodumi
- PDB-4ue3: The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ue3
TitleThe Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / MEMBRANE-BOUND HYDROGENASE / NI-FE HYDROGENASE / HYDROGEN
Function / homology
Function and homology information


hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity ...hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding
Similarity search - Function
[NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase ...[NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / : / NICKEL (II) ION / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEvans, R.M. / Wehlin, S.A.M. / Nomerotskaia, E. / Sargent, F. / Carr, S.B. / Phillips, S.E.V. / Armstrong, F.A.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Mechanism of Hydrogen Activation by [Nife] Hydrogenases.
Authors: Evans, R.M. / Brooke, E.J. / Wehlin, S.A. / Nomerotskaia, E. / Sargent, F. / Carr, S.B. / Phillips, S.E. / Armstrong, F.A.
History
DepositionDec 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 2.0Dec 4, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / audit_conform / chem_comp / database_PDB_matrix / diffrn / diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_database_related / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / 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_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain / _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_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_database_status.SG_entry / _pdbx_database_status.pdb_format_compatible / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_ligand_of_interest / _pdbx_entry_details.sequence_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _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_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_low / _reflns_shell.number_unique_obs / _software.version / _struct.pdbx_CASP_flag / _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.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: Modelling of the water structure, particularly around the active site cavity improved
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
SSS: Hydrogenase-1 small chain
LLL: Hydrogenase-1 large chain
TTT: Hydrogenase-1 small chain
MMM: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,37425
Polymers187,4694
Non-polymers2,90521
Water24,1401340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25710 Å2
ΔGint-377 kcal/mol
Surface area46500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.521, 97.405, 183.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Hydrogenase-1 ... , 2 types, 4 molecules SSSTTTLLLMMM

#1: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 29126.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64608.176 Da / Num. of mol.: 2 / Mutation: R509K
Source method: isolated from a genetically manipulated source
Details: Variant R509K
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACD8, hydrogenase (acceptor)

-
Non-polymers , 10 types, 1361 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#9: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1340 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM Bis tris pH 5.5-5.9, 150 mM NaCl 200 mM Li2SO4 19-21% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→48.75 Å / Num. obs: 317004 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12063 / % possible all: 75.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3usc

3usc


Resolution: 1.4→48.75 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.148 / WRfactor Rwork: 0.128 / SU B: 0.904 / SU ML: 0.035 / Average fsc free: 0.9476 / Average fsc work: 0.9527 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1602 15658 4.941 %
Rwork0.1397 301266 -
all0.141 --
obs-316924 96.835 %
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: 12.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.141 Å20 Å20 Å2
2---0.046 Å20 Å2
3----0.095 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13166 0 87 1340 14593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01313861
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712497
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.64318933
X-RAY DIFFRACTIONr_angle_other_deg1.6331.57429070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55851764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29422.174736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.032152219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7991593
X-RAY DIFFRACTIONr_chiral_restr0.1030.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022973
X-RAY DIFFRACTIONr_nbd_refined0.2340.23034
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.212547
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26875
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.25946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2905
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.26
X-RAY DIFFRACTIONr_nbd_other0.2140.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.236
X-RAY DIFFRACTIONr_mcbond_it1.0321.1296840
X-RAY DIFFRACTIONr_mcbond_other1.0331.136839
X-RAY DIFFRACTIONr_mcangle_it1.4641.6948565
X-RAY DIFFRACTIONr_mcangle_other1.4641.6938566
X-RAY DIFFRACTIONr_scbond_it2.1461.3437021
X-RAY DIFFRACTIONr_scbond_other2.1471.3417011
X-RAY DIFFRACTIONr_scangle_it3.1871.93310287
X-RAY DIFFRACTIONr_scangle_other3.1871.9310275
X-RAY DIFFRACTIONr_lrange_it4.01214.24816366
X-RAY DIFFRACTIONr_lrange_other3.91813.93516098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2869220.28417603X-RAY DIFFRACTION76.9694
1.436-1.4760.25910670.25220644X-RAY DIFFRACTION92.929
1.476-1.5180.21610690.19621128X-RAY DIFFRACTION97.4065
1.518-1.5650.211080.17320571X-RAY DIFFRACTION97.9488
1.565-1.6170.18910680.15819984X-RAY DIFFRACTION98.1262
1.617-1.6730.18810210.14919464X-RAY DIFFRACTION98.3815
1.673-1.7360.169460.13618813X-RAY DIFFRACTION98.4897
1.736-1.8070.1510010.12818054X-RAY DIFFRACTION98.6948
1.807-1.8880.1499250.12417399X-RAY DIFFRACTION98.8669
1.888-1.980.1568900.12416714X-RAY DIFFRACTION99.1049
1.98-2.0870.1547950.12515953X-RAY DIFFRACTION99.1593
2.087-2.2130.1447500.12115161X-RAY DIFFRACTION99.3692
2.213-2.3660.1357180.11714262X-RAY DIFFRACTION99.5018
2.366-2.5550.1426570.11813315X-RAY DIFFRACTION99.6221
2.555-2.7990.1496110.12512327X-RAY DIFFRACTION99.7687
2.799-3.1290.1515610.13211199X-RAY DIFFRACTION99.8641
3.129-3.6120.1455300.1399907X-RAY DIFFRACTION99.9521
3.612-4.4230.144430.1238416X-RAY DIFFRACTION99.9887
4.423-6.2470.1513770.146566X-RAY DIFFRACTION99.9712
6.247-48.750.1642000.163787X-RAY DIFFRACTION99.2038

+
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