[English] 日本語
Yorodumi
- PDB-6g8h: Flavonoid-responsive Regulator FrrA in complex with (R,S)-Naringenin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g8h
TitleFlavonoid-responsive Regulator FrrA in complex with (R,S)-Naringenin
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION / Flavonoids / repressor / TetR-family
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator TetR, C-terminal, Proteobacteria type / AefR-like transcriptional repressor, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
R-naringenin / NARINGENIN / Transcriptional regulatory protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWerner, N. / Hoppen, J. / Palm, G. / Werten, S. / Goettfert, M. / Hinrichs, W.
Citation
Journal: Febs J. / Year: 2021
Title: The induction mechanism of the flavonoid-responsive regulator FrrA.
Authors: Werner, N. / Werten, S. / Hoppen, J. / Palm, G.J. / Gottfert, M. / Hinrichs, W.
#1: Journal: Journal of Bacteriology / Year: 2012
Title: Characterization of the Flavonoid-Responsive Regulator FrrA and Its Binding Sites
Authors: Wenzel, M. / Lang, K. / Gottfert, M.
History
DepositionApr 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / chem_comp / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_database_related / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ref / struct_ref_seq / struct_ref_seq_dif / 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.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.pdbx_tls_group_id / _atom_site.type_symbol / _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_auth_asym_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _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_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_vector / _entity_src_gen.pdbx_host_org_vector_type / _exptl_crystal_grow.pdbx_details / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.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.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_free / _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_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_restr_ncs.dom_id / _refine_ls_restr_ncs.pdbx_auth_asym_id / _refine_ls_restr_ncs.pdbx_number / _refine_ls_restr_ncs.pdbx_type / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_restr_ncs.weight_position / _reflns_shell.pdbx_CC_half / _software.version / _struct.title / _struct_asym.entity_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom.details / _struct_ncs_dom.id / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.dom_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.pdbx_component_id / _struct_ncs_dom_lim.pdbx_refine_code / _struct_ncs_ens.details / _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.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.1May 5, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 2.2Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Jan 17, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
CCC: Transcriptional regulatory protein
DDD: Transcriptional regulatory protein
AAA: Transcriptional regulatory protein
BBB: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,61113
Polymers87,6154
Non-polymers1,9969
Water0
1
CCC: Transcriptional regulatory protein
DDD: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7026
Polymers43,8082
Non-polymers8944
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-10 kcal/mol
Surface area18960 Å2
MethodPISA
2
AAA: Transcriptional regulatory protein
BBB: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9097
Polymers43,8082
Non-polymers1,1015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-6 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.709, 118.709, 78.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CCC
21DDD
32CCC
42AAA
53CCC
63BBB
74DDD
84AAA
95DDD
105BBB
116AAA
126BBB

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPROCCCA20 - 2122 - 194
211GLYGLYPROPRODDDB20 - 2122 - 194
322ARGARGPROPROCCCA21 - 2123 - 194
422ARGARGPROPROAAAC21 - 2123 - 194
533ARGARGPROPROCCCA21 - 2123 - 194
633ARGARGPROPROBBBD21 - 2123 - 194
744ARGARGPROPRODDDB21 - 2123 - 194
844ARGARGPROPROAAAC21 - 2123 - 194
955ARGARGPROPRODDDB21 - 2123 - 194
1055ARGARGPROPROBBBD21 - 2123 - 194
1166ARGARGARGARGAAAC21 - 2133 - 195
1266ARGARGARGARGBBBD21 - 2133 - 195

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

-
Components

#1: Protein
Transcriptional regulatory protein


Mass: 21903.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The sequence represents the crystallized polypeptide
Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria)
Strain: JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110
Gene: blr4322 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q89M71
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-CWE / R-naringenin


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAR / NARINGENIN / Naringenin


Mass: 272.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O5 / Comment: antiinflammatory*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6mg/ml FrrA in 20 mM Na2HPO4, 50 mM imidazole, pH 7.5, 50 mM NaCl with equimolar naringenin in 70% Ethanol. Precipitant 16,5 % PEG 8000; 0.1 M CHES, pH 9.5.
PH range: 7.5 - 9.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.312→118.71 Å / Num. obs: 67523 / % possible obs: 95.2 % / Redundancy: 3.35 % / Biso Wilson estimate: 81.2 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.094 / Net I/σ(I): 9.74
Reflection shellResolution: 2.312→2.54 Å / Redundancy: 2.76 % / Mean I/σ(I) obs: 0.54 / Num. unique obs: 8294 / CC1/2: 0.2 / Rrim(I) all: 1.76 / % possible all: 72.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G87

6g87


Resolution: 2.6→118.709 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 27.121 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 0.444 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions; TLS refinement
RfactorNum. reflection% reflection
Rfree0.2189 1624 4.816 %
Rwork0.1825 32100 -
all0.184 --
obs-33724 99.947 %
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: 75.586 Å2
Baniso -1Baniso -2Baniso -3
1--1.391 Å20 Å20 Å2
2---1.391 Å20 Å2
3---2.783 Å2
Refinement stepCycle: LAST / Resolution: 2.6→118.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 131 0 6199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176175
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.6438541
X-RAY DIFFRACTIONr_angle_other_deg1.3211.57114178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5421.071336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.979151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3051554
X-RAY DIFFRACTIONr_chiral_restr0.0890.2807
X-RAY DIFFRACTIONr_chiral_restr_other0.040.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021485
X-RAY DIFFRACTIONr_nbd_refined0.2120.21261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.25168
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23056
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.23234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.216
X-RAY DIFFRACTIONr_nbd_other0.2260.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3820.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_mcbond_it4.4136.1073096
X-RAY DIFFRACTIONr_mcbond_other4.4086.1073095
X-RAY DIFFRACTIONr_mcangle_it6.4569.1623863
X-RAY DIFFRACTIONr_mcangle_other6.4559.1633864
X-RAY DIFFRACTIONr_scbond_it5.9377.0173223
X-RAY DIFFRACTIONr_scbond_other5.9367.023224
X-RAY DIFFRACTIONr_scangle_it9.26810.2284678
X-RAY DIFFRACTIONr_scangle_other9.26710.234679
X-RAY DIFFRACTIONr_lrange_it10.84371.9516686
X-RAY DIFFRACTIONr_lrange_other10.84371.9686687
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.055636
X-RAY DIFFRACTIONr_ncsr_local_group_20.0870.055840
X-RAY DIFFRACTIONr_ncsr_local_group_30.1170.055605
X-RAY DIFFRACTIONr_ncsr_local_group_40.1220.055613
X-RAY DIFFRACTIONr_ncsr_local_group_50.0860.055820
X-RAY DIFFRACTIONr_ncsr_local_group_60.1240.055588
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11CCCX-RAY DIFFRACTIONLocal ncs0.115320.05006
12DDDX-RAY DIFFRACTIONLocal ncs0.115320.05006
23CCCX-RAY DIFFRACTIONLocal ncs0.086850.05007
24AAAX-RAY DIFFRACTIONLocal ncs0.086850.05007
35CCCX-RAY DIFFRACTIONLocal ncs0.117450.05007
36BBBX-RAY DIFFRACTIONLocal ncs0.117450.05007
47DDDX-RAY DIFFRACTIONLocal ncs0.121960.05007
48AAAX-RAY DIFFRACTIONLocal ncs0.121960.05007
59DDDX-RAY DIFFRACTIONLocal ncs0.085840.05007
510BBBX-RAY DIFFRACTIONLocal ncs0.085840.05007
611AAAX-RAY DIFFRACTIONLocal ncs0.123770.05007
612BBBX-RAY DIFFRACTIONLocal ncs0.123770.05007
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
2.6-2.6670.3681140.38523670.38424810.6450.6491000.384
2.667-2.7410.3461110.36723290.36624400.6810.7281000.366
2.741-2.820.369960.33222240.33323200.7560.7831000.325
2.82-2.9070.303970.29422250.29423220.8430.8491000.279
2.907-3.0020.2951060.24120690.24421750.8810.91000.219
3.002-3.1070.2981030.22220560.22621590.8820.9151000.198
3.107-3.2240.287990.21819640.22120630.8950.9171000.198
3.224-3.3560.2971010.20918820.21319830.870.9241000.187
3.356-3.5050.258990.19718210.219210.9160.93999.94790.182
3.505-3.6760.219870.1917220.19118090.9350.951000.175
3.676-3.8750.225780.17216650.17517430.9360.9551000.159
3.875-4.1090.189880.15815820.1616700.9530.9591000.15
4.109-4.3930.192750.1514700.15315480.9530.96299.80620.147
4.393-4.7440.163770.14613720.14714520.9610.96799.79340.147
4.744-5.1960.206700.14312550.14713250.9560.9671000.144
5.196-5.8080.157640.15611420.15612060.9590.9621000.161
5.808-6.7040.229570.17310240.17610820.9320.94799.90760.178
6.704-8.2040.259540.168470.1659020.9230.95899.88910.175
8.204-11.5750.127290.1126910.1137210.9780.98299.86130.133
11.575-118.7090.164170.2193860.2174110.9710.94998.05350.255
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)
10.48070.50450.28160.54440.3090.17710.0772-0.13630.0280.1193-0.0890.02470.0773-0.02970.01180.18180.06150.01420.2763-0.0420.0099-11.86624.56225.8827
21.306-0.88720.15280.7676-0.00170.13060.0148-0.08580.0785-0.0837-0.0542-0.0196-0.0311-0.00560.03940.2334-0.0170.01960.2189-0.02280.01919.873636.039523.0803
31.16160.3093-0.46720.1374-0.16690.23560.0466-0.001-0.07290.0447-0.0832-0.032-0.08170.02330.03660.19010.02680.01250.24130.01560.012652.758132.7212.0966
40.1247-0.3597-0.10271.06550.29530.42120.04550.0371-0.0569-0.1964-0.11480.1668-0.1827-0.02990.06940.20580.0136-0.03570.253-0.0630.036728.536937.15530.1132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLCCC20 - 213
2X-RAY DIFFRACTION2ALLDDD19 - 213
3X-RAY DIFFRACTION3ALLAAA21 - 213
4X-RAY DIFFRACTION4ALLBBB21 - 213

+
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