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- PDB-5u8x: Crystal structure of Fe-CAO1 -

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Basic information

Entry
Database: PDB / ID: 5u8x
TitleCrystal structure of Fe-CAO1
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / beta propeller / dioxygenase / resveratrol / carotenoid oxygenase
Function / homologycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding / BENZOIC ACID / : / Carotenoid cleavage oxygenase 1
Function and homology information
Biological speciesNeurospora crassa OR74A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.165 Å
AuthorsSui, X. / Palczewski, K. / Banerjee, S. / Kiser, P.D.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY020551 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA157735 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM77387 United States
Burroughs Wellcome Fund1015187 United States
Department of Veterans Affairs (VA, United States)BX002683 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Spectroscopy of Alkene-Cleaving Dioxygenases Containing an Atypically Coordinated Non-Heme Iron Center.
Authors: Sui, X. / Weitz, A.C. / Farquhar, E.R. / Badiee, M. / Banerjee, S. / von Lintig, J. / Tochtrop, G.P. / Palczewski, K. / Hendrich, M.P. / Kiser, P.D.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _struct_keywords.text
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn / entity / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns_shell / software / struct_asym / struct_conn / struct_keywords / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _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 / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal_grow.pdbx_details / _pdbx_audit_support.funding_organization / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_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_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns_shell.number_unique_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Ligand geometry
Details: Metal occupancy was refined and the piceatannol dictionary file from CCP4 was used.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 3.0Jul 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / entity / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conn / struct_keywords / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _entity.pdbx_number_of_molecules / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_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_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _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_high / _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.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr.type / _reflns.d_resolution_high / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.text
Description: Model completeness
Details: Additional waters of mechanistic relevance were added. An active site site chain conformation was updated.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carotenoid oxygenase 1
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,72315
Polymers237,9924
Non-polymers73211
Water20,5731142
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3017
Polymers118,9962
Non-polymers3055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4238
Polymers118,9962
Non-polymers4276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.908, 100.908, 448.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111LEULEU30 - 52630 - 526
211LEULEU30 - 52630 - 526
322PROPRO30 - 52530 - 525
422PROPRO30 - 52530 - 525
533LEULEU30 - 52630 - 526
633LEULEU30 - 52630 - 526
744PROPRO30 - 52530 - 525
844PROPRO30 - 52530 - 525
955LEULEU30 - 52630 - 526
1055LEULEU30 - 52630 - 526
1166PROPRO30 - 52530 - 525
1266PROPRO30 - 52530 - 525

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Carotenoid oxygenase 1


Mass: 59497.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa OR74A (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: cao-1, NCU07008 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S860
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: Sodium polyacrylate, HEPES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.722 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.165→50.14 Å / Num. obs: 128129 / % possible obs: 89.8 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 17
Reflection shellResolution: 2.17→2.3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 12800 / % possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OU9

4ou9


Resolution: 2.165→50.138 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.22 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.176
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 6323 4.937 %RANDOM
Rwork0.1807 121762 --
all0.182 ---
obs-128085 89.813 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.582 Å20.291 Å20 Å2
2--0.582 Å2-0 Å2
3----1.887 Å2
Refinement stepCycle: LAST / Resolution: 2.165→50.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15941 0 35 1142 17118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01216522
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614974
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.66722468
X-RAY DIFFRACTIONr_angle_other_deg0.3151.58234558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17351997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.3522.074121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.941102546
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.56110839
X-RAY DIFFRACTIONr_chiral_restr0.0460.22288
X-RAY DIFFRACTIONr_chiral_restr_other0.0160.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024009
X-RAY DIFFRACTIONr_nbd_refined0.1860.22750
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.213731
X-RAY DIFFRACTIONr_nbtor_refined0.1780.27859
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.28468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21017
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1080.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.221
X-RAY DIFFRACTIONr_nbd_other0.2270.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.29
X-RAY DIFFRACTIONr_mcbond_it1.924.1957982
X-RAY DIFFRACTIONr_mcbond_other1.924.1957982
X-RAY DIFFRACTIONr_mcangle_it3.0977.5369978
X-RAY DIFFRACTIONr_mcangle_other3.0997.5379979
X-RAY DIFFRACTIONr_scbond_it2.4364.5028540
X-RAY DIFFRACTIONr_scbond_other2.4354.5028541
X-RAY DIFFRACTIONr_scangle_it4.1388.13212489
X-RAY DIFFRACTIONr_scangle_other4.1378.13212490
X-RAY DIFFRACTIONr_lrange_it5.75241.45717924
X-RAY DIFFRACTIONr_lrange_other5.73141.4717859
X-RAY DIFFRACTIONr_ncsr_local_group_10.0540.0516394
X-RAY DIFFRACTIONr_ncsr_local_group_20.050.0516469
X-RAY DIFFRACTIONr_ncsr_local_group_30.0560.0516422
X-RAY DIFFRACTIONr_ncsr_local_group_40.050.0516377
X-RAY DIFFRACTIONr_ncsr_local_group_50.050.0516418
X-RAY DIFFRACTIONr_ncsr_local_group_60.0520.0516396
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.053770.05011
12AX-RAY DIFFRACTIONLocal ncs0.053770.05011
23AX-RAY DIFFRACTIONLocal ncs0.050030.05011
24AX-RAY DIFFRACTIONLocal ncs0.050030.05011
35AX-RAY DIFFRACTIONLocal ncs0.05640.0501
36AX-RAY DIFFRACTIONLocal ncs0.05640.0501
47AX-RAY DIFFRACTIONLocal ncs0.049750.05011
48AX-RAY DIFFRACTIONLocal ncs0.049750.05011
59AX-RAY DIFFRACTIONLocal ncs0.050250.0501
510AX-RAY DIFFRACTIONLocal ncs0.050250.0501
611AX-RAY DIFFRACTIONLocal ncs0.052110.0501
612AX-RAY DIFFRACTIONLocal ncs0.052110.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.165-2.2210.4192630.41449900.415104160.830.82250.4320.424
2.221-2.2820.3723030.35957610.36101130.9150.91559.96240.354
2.282-2.3480.3453500.32966540.3398890.9430.94270.82620.311
2.348-2.420.334080.32177490.32295300.9330.94385.59290.3
2.42-2.50.2924540.26886260.26993360.9540.96197.25790.237
2.5-2.5870.264430.23584270.23790410.9620.96898.10860.204
2.587-2.6840.2284230.2180340.21186010.9670.97498.32580.18
2.684-2.7940.2454150.21378890.21584240.9640.97498.57550.185
2.794-2.9180.2413870.21175810.21280630.9640.97698.82180.19
2.918-3.0590.2553690.20572920.20777400.9590.97798.97930.186
3.059-3.2240.2363530.19768970.19973120.9630.97999.15210.181
3.224-3.4190.2043360.17765960.17969780.9750.98299.34080.166
3.419-3.6540.1843200.16162270.16365790.980.98599.51360.154
3.654-3.9450.1712980.14457990.14561170.9820.98899.6730.14
3.945-4.3190.1512760.12954030.1356860.9870.9999.87690.128
4.319-4.8240.1392540.11849270.11951840.9890.99299.94210.121
4.824-5.5620.1552270.1343760.13146040.9890.99299.97830.132
5.562-6.7910.1731940.15737510.15839480.9840.98899.9240.157
6.791-9.5170.1481550.14229630.14231180.9870.9881000.149
9.517-50.1380.189950.16818200.16919160.9780.98199.94780.192

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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

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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

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