[English] 日本語
Yorodumi
- PDB-5cdn: 2.8A structure of etoposide with S.aureus DNA gyrase and DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cdn
Title2.8A structure of etoposide with S.aureus DNA gyrase and DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EVP / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsBax, B.D. / Srikannathasan, V. / Chan, P.F.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, ...Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, C.E. / Tanner, R. / Theobald, A.J. / Stavenger, R.A. / Bax, B.D. / Gwynn, M.N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
Authors: Srikannathasan, V. / Wohlkonig, A. / Shillings, A. / Singh, O. / Chan, P.F. / Huang, J. / Gwynn, M.N. / Fosberry, A.P. / Homes, P. / Hibbs, M. / Theobald, A.J. / Spitzfaden, C. / Bax, B.D.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
G: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
O: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
N: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
P: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,17930
Polymers328,11816
Non-polymers3,06114
Water7,422412
1
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
G: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
O: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,74117
Polymers164,0598
Non-polymers1,6829
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21370 Å2
ΔGint-142 kcal/mol
Surface area58130 Å2
MethodPISA
2
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
N: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
P: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,43813
Polymers164,0598
Non-polymers1,3795
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20370 Å2
ΔGint-119 kcal/mol
Surface area57800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.782, 170.081, 124.540
Angle α, β, γ (deg.)90.00, 102.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA gyrase subunit ... , 2 types, 8 molecules ACRTBDSU

#1: Protein
DNA gyrase subunit A /


Mass: 54664.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#2: Protein
DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21274.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

-
DNA chain , 2 types, 8 molecules EFVWGONP

#3: DNA chain
DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP**GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')


Mass: 2451.630 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*C)-3')


Mass: 3639.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 426 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-EVP / (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside / Etoposide / VP-16 / Etoposide


Mass: 588.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H32O13 / Comment: medication, chemotherapy*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 150mM Bis Tris pH6.2, 11% PEG 5000 MME / PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 87189 / % possible obs: 96.6 % / Redundancy: 3 % / Biso Wilson estimate: 74.37 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.852.90.39943121.07296.1
2.85-2.92.90.40543751.0697
2.9-2.9630.32943891.13797.9
2.96-3.0230.2944001.10197.8
3.02-3.0830.2743871.14797.7
3.08-3.1530.23643981.1997.7
3.15-3.2330.20943861.18197.7
3.23-3.3230.17444041.16197.4
3.32-3.4230.14943731.13797.1
3.42-3.5330.15343411.39296.6
3.53-3.653.10.1243701.07997.2
3.65-3.830.1243531.28996.8
3.8-3.9730.10643191.22395.8
3.97-4.183.10.08643781.00296.7
4.18-4.443.10.08643751.06596.7
4.44-4.7930.08843701.12596.6
4.79-5.2730.09343711.20596.6
5.27-6.0330.08143630.95996
6.03-7.5830.06442890.90995.1
7.58-4030.0642360.99891.7

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.79→39.35 Å / Cor.coef. Fo:Fc: 0.8897 / Cor.coef. Fo:Fc free: 0.8708 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3484 4 %RANDOM
Rwork0.2132 ---
obs0.2143 87157 96.13 %-
Displacement parametersBiso mean: 77.78 Å2
Baniso -1Baniso -2Baniso -3
1--7.0169 Å20 Å2-0.722 Å2
2--24.5222 Å20 Å2
3----17.5053 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.79→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20783 1589 202 412 22986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00823154HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9831653HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8098SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes594HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3212HARMONIC5
X-RAY DIFFRACTIONt_it23154HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion18.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3087SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25811SEMIHARMONIC4
LS refinement shellResolution: 2.79→2.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2697 247 4.15 %
Rwork0.2387 5704 -
all0.24 5951 -
obs--96.13 %
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)
11.0699-0.04410.2071.18320.62353.45250.2435-0.6406-0.46540.6905-0.0287-0.21490.33270.2721-0.2149-0.0290.0112-0.0101-0.17570.0912-0.050242.8814-51.409982.4939
21.626-0.597-0.08273.3328-0.21930.6385-0.07870.23660.3077-0.25110.01980.2526-0.059-0.04980.0589-0.3489-0.04240.041-0.21650.02820.21529.2662-26.212852.4395
30.57861.77341.63957.92360.40040.68580.00470.0696-0.104-0.0094-0.05540.1848-0.0331-0.10130.0507-0.2760.0761-0.1107-0.2743-0.0230.571331.00526.086456.7863
45.73950.15461.293.44352.05090.2896-0.094-0.1502-0.0904-0.15780.09020.3358-0.10190.15270.0039-0.08160.03590.0268-0.2582-0.01710.169447.577617.983563.9871
55.28491.7317-3.28651.33151.6416-0.06890.0365-0.33320.09840.4584-0.02880.1029-0.1806-0.4843-0.0077-0.07960.04310.2522-0.12970.15190.276223.5033-44.635579.5754
64.15010.28390.41230.12290.40592.7824-0.07120.7903-0.2304-0.8076-0.20120.4757-0.4702-0.50340.27240.12560.0802-0.1921-0.2289-0.1266-0.091165.5732-52.412337.2554
71.13920.3204-0.51183.25220.25971.2846-0.0407-0.12750.2179-0.0815-0.0089-0.17430.06060.11670.0496-0.28130.06670.0303-0.2566-0.01450.122878.2814-27.721968.6631
8-0.5138-2.43741.07183.3707-1.88651.0061-0.02380.0707-0.207-0.0127-0.1713-0.26530.13280.1310.1951-0.0478-0.03520.1081-0.1670.02290.38479.75294.225764.7767
94.897-1.18110.12414.18380.30811.10320.06990.10270.1878-0.4486-0.0793-0.1811-0.5676-0.2150.00940.015-0.02690.0702-0.2810.00430.117163.749717.652158.8366
106.2681-1.6381-3.22360.83922.62894.9282-0.14460.42350.071-0.36780.1534-0.13160.03750.403-0.00880.1525-0.0430.2057-0.3227-0.05580.167884.7943-46.846442.3415
110.7281.66971.70826.7928-0.36461.9554-0.11780.1212-0.37540.0719-0.06340.48850.3432-0.44660.1812-0.14240.20420.0846-0.3977-0.0025-0.009475.0464-48.481560.4799
121.69383.1422-0.84686.76370.2261.9438-0.1734-0.1361-0.5418-0.41210.1182-0.16180.3893-0.2710.0552-0.3116-0.10820.0253-0.3112-0.02380.31931.0931-47.266360.3007
130.302-0.8993-0.62910.68040.31973.9334-0.1950.3531-0.2586-0.27940.01960.23710.44630.0620.17550.0108-0.11970.0921-0.0658-0.11010.140227.8542-53.241432.679
141.71060.67090.61581.7883-0.27944.0335-0.085-0.162-0.51430.11410.15450.05640.82640.0659-0.06950.11280.17060.1147-0.08620.11320.09575.8627-55.079588.5412
153.9088-1.2949-0.53711.62910.60816.09380.0059-0.63770.63240.9483-0.0252-0.0904-0.5874-0.5180.01930.03650.0008-0.0999-0.3043-0.2264-0.060478.5894-7.124321.2325
162.4631-1.0862-0.07263.46680.4320.8468-0.06950.33150.1467-0.0544-0.0437-0.3858-0.00510.06010.1132-0.319-0.0712-0.0187-0.20610.05620.111992.6145-33.0876-8.1879
172.9882-0.2440.27362.8045-2.8746-0.0224-0.08040.2081-0.0759-0.0125-0.0747-0.07060.16070.22920.1552-0.0583-0.02940.185-0.20080.02470.290290.6271-64.9421-2.5587
185.91121.4574-1.11642.1938-0.93810.6063-0.0693-0.0053-0.0274-0.2660.005-0.19420.55820.01270.0642-0.05850.06140.1527-0.32640.04930.204873.8253-76.68454.0894
193.0115-0.23392.01010.48223.91093.4397-0.0564-0.41160.08820.35820.0978-0.11820.12360.3119-0.0413-0.0006-0.0107-0.4059-0.2323-0.14160.313897.8861-13.649818.199
204.7465-0.5318-1.81252.30340.07562.928-0.16970.53290.3744-0.91110.0865-0.29650.17810.39040.08320.0567-0.00940.1984-0.1950.1526-0.101656.0756-6.9464-24.22
211.85340.11760.29883.2235-0.55071.3367-0.0434-0.1765-0.1170.21850.12750.1724-0.1019-0.1623-0.084-0.23430.07720.1508-0.25520.0275-0.005743.4202-30.81247.6917
221.0346-2.32714.20454.39560.45721.77990.0143-0.03070.0950.1291-0.07530.2076-0.06-0.30270.061-0.1187-0.06340.1471-0.25150.06580.370941.8421-62.69344.4577
232.00570.70530.00344.0716-1.21440.0435-0.04140.0311-0.1473-0.60720.0639-0.05230.5498-0.1981-0.02250.0124-0.05260.0684-0.28150.00360.253157.6877-76.3147-1.2055
244.3308-0.02450.74273.1657-1.83090.5534-0.04450.43150.0902-0.2541-0.07180.319-0.1348-0.31020.11630.0374-0.0246-0.0779-0.16350.11920.091837.0076-12.4869-19.0623
251.755-2.5633-0.99616.79320.15082.2188-0.17420.04560.51990.44830.1585-0.2576-0.24170.17030.0157-0.20520.09620.1594-0.3794-0.03730.157346.3367-10.1601-0.8747
263.17233.85120.81069.6289-1.42152.3093-0.2420.14010.6944-0.32050.3079-0.1779-0.14130.2619-0.0659-0.3682-0.088-0.0287-0.32150.07520.512290.395-11.5157-1.0831
27-0.0029-0.9718-0.00642.0321-3.33111.9356-0.06340.25250.235-0.2985-0.0498-0.1056-0.31950.05680.1132-0.0032-0.2473-0.0563-0.03330.25650.190993.8425-7.5619-28.9933
28-0.06372.70780.35722.63962.13315.7042-0.0327-0.54830.48350.43220.0518-0.1766-0.25380.1046-0.01910.27970.2915-0.0236-0.0507-0.2356-0.13145.8131-3.291726.9277
294.58970.3065-6.149510.77531.32286.2929-0.09150.0834-0.01530.02440.1428-0.02340.19580.0524-0.0513-0.3550.11670.04980.3569-0.09750.33853.1093-48.751459.6448
301.99611.90814.538910.5842-1.69716.1697-0.04810.17250.15180.27410.00540.0527-0.1876-0.05320.0427-0.28010.0836-0.09040.1118-0.01980.4368.4633-10.0145-1.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|417 - B|608 B|1001 - B|1006 }
2X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|490 }
3X-RAY DIFFRACTION3{ A|370 - A|379 A|445 - A|460 }
4X-RAY DIFFRACTION4{ A|380 - A|444 }
5X-RAY DIFFRACTION5{ A|10 - A|28 B|609 - B|636 }
6X-RAY DIFFRACTION6{ D|417 - D|608 D|1001 - D|1005 }
7X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|369 C|461 - C|490 }
8X-RAY DIFFRACTION8{ C|370 - C|379 C|445 - C|460 }
9X-RAY DIFFRACTION9{ C|380 - C|444 }
10X-RAY DIFFRACTION10{ C|11 - C|28 D|609 - D|636 }
11X-RAY DIFFRACTION11{ E|1 - E|8 O|2013 - O|2019 }
12X-RAY DIFFRACTION12{ G|2013 - G|2019 F|1 - F|8 }
13X-RAY DIFFRACTION13{ A|245 - A|327 }
14X-RAY DIFFRACTION14{ C|245 - C|327 }
15X-RAY DIFFRACTION15{ S|417 - S|608 S|1005 - S|1005 }
16X-RAY DIFFRACTION16{ R|29 - R|244 R|328 - R|369 R|461 - R|490 }
17X-RAY DIFFRACTION17{ R|370 - R|379 R|445 - R|460 }
18X-RAY DIFFRACTION18{ R|380 - R|444 }
19X-RAY DIFFRACTION19{ R|10 - R|28 S|609 - S|636 }
20X-RAY DIFFRACTION20{ U|417 - U|608 U|1001 - U|1005 }
21X-RAY DIFFRACTION21{ T|29 - T|244 T|328 - T|369 T|461 - T|490 }
22X-RAY DIFFRACTION22{ T|370 - T|379 T|445 - T|460 }
23X-RAY DIFFRACTION23{ T|380 - T|444 }
24X-RAY DIFFRACTION24{ T|10 - T|28 U|609 - U|636 }
25X-RAY DIFFRACTION25{ V|1 - V|8 W|2013 - W|2019 }
26X-RAY DIFFRACTION26{ N|2013 - N|2019 W|1 - W|8 }
27X-RAY DIFFRACTION27{ R|245 - R|327 }
28X-RAY DIFFRACTION28{ T|245 - T|327 }
29X-RAY DIFFRACTION29{ E|2009 - E|2012 F|2009 - F|2012 I|1 I|21 }
30X-RAY DIFFRACTION30{ N|2009 - N|2012 P|2009 - P|2012 I|201 I|221 }

+
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