[English] 日本語
Yorodumi
- PDB-7ugw: M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ugw
TitleM. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin
Components
  • DNA (46-MER)
  • DNA gyrase subunit A
  • DNA gyrase subunit B
  • evybactin
KeywordsISOMERASE/ANTIBIOTIC/DNA / Topoisomerase / inhibitor / natural product / ISOMERASE-ANTIBIOTIC-DNA complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Photorhabdus noenieputensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHauk, G. / Imai, Y. / Lewis, K. / Berger, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI118687 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA077373 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35263778 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis.
Authors: Imai, Y. / Hauk, G. / Quigley, J. / Liang, L. / Son, S. / Ghiglieri, M. / Gates, M.F. / Morrissette, M. / Shahsavari, N. / Niles, S. / Baldisseri, D. / Honrao, C. / Ma, X. / Guo, J.J. / Berger, J.M. / Lewis, K.
History
DepositionMar 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_database_status / pdbx_entity_instance_feature / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_molecule.prd_id / _pdbx_molecule_features.prd_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.d_res_low / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.version / _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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet.number_strands
Description: Chirality error
Details: Our collaborators recently identified that evybactin contains D-Methylhistidine, rather than the L- isoform. The coordinates have been updated to reflect this.
Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B
V: DNA (46-MER)
E: evybactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,7848
Polymers183,7366
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-123 kcal/mol
Surface area63920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.075, 105.088, 250.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein DNA gyrase subunit A / Type IIA topoisomerase subunit GyrA


Mass: 55870.184 Da / Num. of mol.: 2 / Mutation: Y129F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrA, Rv0006, MTCY10H4.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG47, DNA topoisomerase (ATP-hydrolysing)
#2: Protein DNA gyrase subunit B


Mass: 28129.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrB, Rv0005, MTCY10H4.03 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG45, DNA topoisomerase (ATP-hydrolysing)
#3: DNA chain DNA (46-MER)


Mass: 14228.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein/peptide evybactin


Type: Peptide-like / Class: Antibiotic / Mass: 1508.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Photorhabdus noenieputensis (bacteria) / References: BIRD: PRD_002540
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7-12% PEG10K; 100mM MES pH 6.0; 200mM magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3→48.46 Å / Num. obs: 44612 / % possible obs: 99.64 % / Redundancy: 4 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1395 / Rpim(I) all: 0.06624 / Rrim(I) all: 0.1549 / Net I/σ(I): 10.44
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 4388 / CC1/2: 0.822

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS8

5bs8


Resolution: 3→48.44 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276 1809 4.06 %
Rwork0.2177 42778 -
obs0.22 44587 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.48 Å2
Refinement stepCycle: LAST / Resolution: 3→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11427 945 2 0 12374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312664
X-RAY DIFFRACTIONf_angle_d1.540217331
X-RAY DIFFRACTIONf_chiral_restr0.07011965
X-RAY DIFFRACTIONf_plane_restr0.0122126
X-RAY DIFFRACTIONf_dihedral_angle_d19.35774830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.43621370.33053237X-RAY DIFFRACTION99.73
3.08-3.170.36281360.3043217X-RAY DIFFRACTION99.76
3.17-3.270.31231390.28693264X-RAY DIFFRACTION99.71
3.27-3.390.32361350.26883220X-RAY DIFFRACTION99.53
3.39-3.530.3051390.24553278X-RAY DIFFRACTION99.82
3.53-3.690.2721360.23833215X-RAY DIFFRACTION99.67
3.69-3.880.2721400.21533301X-RAY DIFFRACTION99.42
3.88-4.120.26681380.20483252X-RAY DIFFRACTION99.74
4.12-4.440.26731380.18593284X-RAY DIFFRACTION99.59
4.44-4.890.24031410.17883320X-RAY DIFFRACTION99.68
4.89-5.60.24021400.19243307X-RAY DIFFRACTION99.77
5.6-7.050.30051410.22033375X-RAY DIFFRACTION99.72
7.05-48.440.23151490.18783508X-RAY DIFFRACTION99.81
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)
11.027591474390.144332907066-0.1299748410590.235181330633-0.176893926820.2557751702950.0802164397599-0.260942831808-0.04376510915530.0422458588592-0.0604848183077-0.0416885826415-0.08090766768410.0401319949076-9.57066052597E-50.351334860527-0.0146919394604-0.01209773469770.3588227871650.03237266681760.25421755228947.333418352639.132934027944.1703222392
20.04846887942240.0165635345267-0.236125381720.3552640314930.4949663571531.230609682650.1207821098480.0180419459461-0.279142898276-0.240754008269-0.00343253069524-0.154489542289-0.4433639846910.1501882077120.2630717307710.33993359415-0.03342625259-0.03579744012581.097919350910.5381068755970.17899224356341.714075287526.650460152369.3177978473
30.1495333235740.01635037940360.3189151900720.1506962529720.2165827837230.903172318141-0.0805043302039-0.270412494895-0.265562831390.337441000959-0.459418089313-0.4261170391030.100567102653-0.27561248229-0.5726058104350.7030516743710.007102468236320.06459961751991.124890318010.4534516424660.58688111199238.339142523725.401213084775.6243271278
40.103571825289-0.1421727194740.017374185840.12056724117-0.1613717003380.2985164277760.153803342513-0.156996764631-0.161941545227-0.0921169771989-0.199383389426-0.110657207908-0.06967754616250.1850005231430.01229131609430.375973756531-0.0517865614293-0.06221470770590.5537146626360.1534408749880.39245809548455.974535411330.235336137858.2729603004
50.2071135777020.1247015242930.04077238109130.196386480169-0.2496533710020.021388314530.1517659275880.1220861404290.299481810197-0.0763270661147-0.296052814904-0.1817100714570.04897464472760.3076210862960.0002668021678240.528109356825-0.08943561136350.008624820946310.4062031274330.03979541188970.37041542812552.225127637861.617877608730.381204249
60.33770892445-0.0258784733223-0.04746990254190.183371709654-0.1461027705640.0283963360282-0.04078525938430.3530918151120.4832905901880.07256469276930.103335863067-0.190150959588-0.2075399414430.3626643718970.005952193980610.752112365652-0.07819506921310.02762224097590.4699692739720.1115930497370.52301399097440.153380040576.719989919815.8542527469
70.2980234027440.007891376644970.2427762129430.01582853464040.04715205300420.2418087275610.0552606388025-0.7380558157780.4864272258970.228154999676-0.0683769586679-0.248763005761-0.3192045444820.2817748533910.1148619236740.621471874312-0.0224661329730.03471465334950.609955466384-0.1068353011120.35516944258553.251221130555.215127055352.1155211883
80.06823890135370.0708907659327-0.1230987885520.0172150138527-0.04633163002510.06985065396540.06808274118480.0241164055743-0.253635018282-0.0865040176633-0.01173881363910.1177687044430.3181474302330.04521941505296.77088804341E-70.546961946354-0.028604905425-0.03981219838540.4084758115-0.1147599691080.78447024073433.40496619610.13380944307323.2311635282
90.4338496391630.159245246321-0.06846123609150.07136938428910.07986054756510.372213575858-0.0313378182538-0.00773410652226-0.574041459604-0.1240287106650.0513490389868-0.1677540059120.0269813911403-0.059111864183-0.0005099210006540.4126169275690.03986493264350.003018413735410.2799903639830.06255060377370.6923073427943.97955695815.4236193006429.3830370373
100.113813728448-0.0727054885026-0.2121789160630.1504391533990.03870784128290.234039019490.1448893405590.4313243409220.08474070244540.00418587200224-0.110646446002-0.0289384069642-0.0469512922982-0.00355146878662.60903910768E-90.4541941335870.02510254955160.006239457042820.494474667545-0.0500801467050.50527657486638.313437876327.526983289510.4126529278
110.0197070224430.030486730086-0.02563218598030.0953506812657-0.04263110239470.0391136952756-0.06366862186380.1206314680220.0745199932942-0.2722200480280.261631830918-0.056399643509-0.0704968414290.2595166615593.42397213093E-60.5855962936880.0517253234322-0.005736938173690.502353463269-0.03246557923210.82465963786748.42401738428.9180613491615.5478511734
120.271350614252-0.0384038462177-0.0731659609831-0.0100740260610.02191425322410.008350660768380.09873023182760.04334084112940.05103459369690.2782378448410.0661304070914-0.0644164772274-0.11123892674-0.04170901996942.12450453018E-70.4280972586720.04349856405010.01046373567240.5058580930070.1413415746840.82568591787563.024668081517.839167936631.9460582577
130.2294844094720.166237657514-0.004838076104350.05059179240540.102582507820.218354466603-0.05851630004280.1228258625890.07743253560410.0385394854840.2043488181540.157273222365-0.134017099592-0.3123892703280.001018940785750.2772649935210.05361174491730.05106076521920.2246178319990.08118236469730.2776619074998.7250265723134.810201175736.7205839114
140.185107995442-0.147973646197-0.03821122206860.2523647991580.1637406227440.219765503916-0.0592684301842-0.0777417419467-0.1879705989570.04862405705530.02898782727810.003789632328750.02814222766750.0382115486859-4.11120459196E-80.3364142203820.03193677274820.01290713346350.3024194345940.05545171518330.32011549131819.958924479129.394991172125.2712542627
150.358465700416-0.186249996766-0.09062591031760.418929020501-0.1752992770490.1021226405960.09828063149780.036641092754-0.128937384607-0.119942697386-0.02729278893210.0480691076795-0.0275081546924-0.225526315405-1.25095323642E-90.391686811480.0242103350222-0.05775545987530.4002251993010.04399414950920.3542034435340.18432551659732.929759988418.9524218488
160.1178749203520.003741695296710.06725149232210.286869497753-0.02230113202760.006182110350120.06734165295370.0438940458078-0.121290258308-0.003774080083570.009098138988290.2213544305070.113546148085-0.2360182581790.0005901118255270.405093127368-0.0357096063296-0.08093802281610.259518152016-0.004242455741360.60694763145210.76427509941.7183513452716.6215150474
170.1718147540460.0983658577870.177345462920.3621367326270.1309767461110.402395698582-0.0550883900618-0.225195380104-0.260729892212-0.1138881792740.3109757210080.07043412710970.04340652215850.0894821305890.0004781751272380.414432013994-0.0363615160304-0.05416659619770.4011194236140.04440704217580.5109842644545.499799690688.9703607740918.1548907961
180.227329970390.530862013370.3287824191870.8271304451470.1811324128330.006785910799570.1763526444840.2062058426430.2877280839180.359627202092-0.203260762970.526527224180.0183134488692-0.191914245003-0.1394653596250.4450928930110.0622920108174-0.007828457661620.3679689844150.1987028308480.4628166286183.9751246602655.357690958316.3894415059
190.3387909505970.0312680080382-0.0647457610131-0.0102066707916-0.0260143558649-0.0120702723645-0.06045753875370.1720989778750.376766879412-0.0446553176842-0.003761653486080.106610739811-0.342792897304-0.120206367628-0.05287061419730.766251169197-0.0146210963331-0.02332731267310.4388984054870.1992784657660.69738403731617.354102764176.243723213.6088997466
200.01107392735140.07740041580810.07610341861740.06318469915010.06899416825980.105501006917-0.003909018821440.2631063682160.0251242239911-0.370459893498-0.08465406951770.155566538401-0.0441997117440.2221874951791.20665605907E-70.499156197117-0.0329816479971-0.01383961868270.485856039126-0.008995317685160.3168661292652.5564343387536.04994016617.23806468892
210.0290797514885-0.06044733187630.005997060931540.0578230584103-0.03005844681614.11373376962E-5-0.09367234920820.3509748477390.4173978208070.0279441119981-0.256084769208-0.140915550320.4791520134050.3026131230541.16574401169E-60.6901557122670.02046586417210.02148520475710.8256779800270.1943435280640.56566662100521.972766337520.792458649171.2308784746
220.206399554769-0.204183018182-0.1118484178530.246229350949-0.1031995893350.345509054464-0.0708912586377-0.319065907402-0.238692612124-0.02452855288150.0719149729150.1115334529230.04810733773860.02119185659388.80840417215E-90.542710832792-0.03324858565710.02704481191560.633169379060.2279819489640.49479202828614.134585389118.672686514459.8092756558
230.439683198457-0.1883627869450.1335894245870.199479933046-0.2422114704940.3795775202120.002050507587-0.201930406477-0.01373997420170.09361253855710.01942215003090.250725015637-0.0745397625922-0.1277002102742.91191109571E-100.463357255202-0.02375452108210.009669890930350.5698650765410.1442239303320.4062081870516.3397515275432.539672760355.8214452114
24-0.0202017020339-0.03159211304510.04087881914980.144207150942-0.03420304566480.579409188036-0.1418051272310.255420149683-0.333200832596-0.2286990797070.197580441235-0.569944150350.4507162669020.7383462138930.00101952063970.627097421391-0.07986913110180.009171495993320.6509404672030.09686442618980.8569897123819.2827895839612.410534149237.5181982047
25-0.0307219971150.4232248843130.2834170052230.341250234150.1904149185060.0501594862808-0.0470525254958-0.535085282438-0.7854470392440.0611297504433-0.01023188631870.05566532166320.0343054584686-0.0729577512759-1.293373398180.4803834581080.00901670043442-0.04248466579350.5756385953360.3020042235310.64556784973735.689500908318.507586228145.545227159
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 260 )AA15 - 2601 - 246
22chain 'A' and (resid 261 through 291 )AA261 - 291247 - 275
33chain 'A' and (resid 292 through 323 )AA292 - 323276 - 307
44chain 'A' and (resid 324 through 357 )AA324 - 357308 - 341
55chain 'A' and (resid 358 through 399 )AA358 - 399342 - 383
66chain 'A' and (resid 400 through 470 )AA400 - 470384 - 454
77chain 'A' and (resid 471 through 501 )AA471 - 501455 - 485
88chain 'B' and (resid 425 through 460 )BB425 - 4601 - 33
99chain 'B' and (resid 461 through 564 )BB461 - 56434 - 137
1010chain 'B' and (resid 565 through 625 )BB565 - 625138 - 198
1111chain 'B' and (resid 626 through 640 )BB626 - 640199 - 213
1212chain 'B' and (resid 641 through 675 )BB641 - 675214 - 248
1313chain 'C' and (resid 14 through 72 )CD14 - 721 - 59
1414chain 'C' and (resid 73 through 142 )CD73 - 14260 - 129
1515chain 'C' and (resid 143 through 246 )CD143 - 246130 - 233
1616chain 'C' and (resid 247 through 304 )CD247 - 304234 - 291
1717chain 'C' and (resid 305 through 357 )CD305 - 357292 - 344
1818chain 'C' and (resid 358 through 398 )CD358 - 398345 - 385
1919chain 'C' and (resid 399 through 470 )CD399 - 470386 - 457
2020chain 'C' and (resid 471 through 500 )CD471 - 500458 - 487
2121chain 'D' and (resid 425 through 453 )DE425 - 4531 - 23
2222chain 'D' and (resid 454 through 521 )DE454 - 52124 - 91
2323chain 'D' and (resid 522 through 674 )DE522 - 67492 - 232
2424chain 'V' and (resid 1 through 15 )VF1 - 15
2525chain 'V' and (resid 16 through 46 )VF16 - 46

+
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