[English] 日本語
Yorodumi
- PDB-5oe6: Crystal structure of the N-terminal domain of PqsA in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oe6
TitleCrystal structure of the N-terminal domain of PqsA in complex with 6-fluoroanthraniloyl-AMP (crystal form 1)
ComponentsAnthranilate--CoA ligase
KeywordsLIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily / Fluor / 6FABA / 6-fluoroanthranilate / 6-fluoroanthraniloyl-AMP / 6FABA-AMP
Function / homology
Function and homology information


anthranilate-CoA ligase / anthranilate-CoA ligase activity / acid-thiol ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
6-fluoroanthraniloyl-AMP / TRIETHYLENE GLYCOL / Anthranilate--CoA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsWitzgall, F. / Ewert, W. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2017
Title: Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.
Authors: Witzgall, F. / Ewert, W. / Blankenfeldt, W.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Anthranilate--CoA ligase
B: Anthranilate--CoA ligase
C: Anthranilate--CoA ligase
D: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6689
Polymers177,5814
Non-polymers2,0885
Water26,0141444
1
A: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0303
Polymers44,3951
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.558, 84.130, 138.212
Angle α, β, γ (deg.)90.000, 92.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 12 or (resid 13...
21(chain B and (resid 3 through 12 or (resid 13...
31(chain C and (resid 3 through 12 or (resid 13...
41(chain D and (resid 3 through 18 or resid 20...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPHEPHE(chain A and (resid 3 through 12 or (resid 13...AA3 - 123 - 12
12ARGARGARGARG(chain A and (resid 3 through 12 or (resid 13...AA1313
13THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
14THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
15THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
16THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
17THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
18THRTHRASPASP(chain A and (resid 3 through 12 or (resid 13...AA3 - 3993 - 399
21THRTHRPHEPHE(chain B and (resid 3 through 12 or (resid 13...BB3 - 123 - 12
22ARGARGARGARG(chain B and (resid 3 through 12 or (resid 13...BB1313
23SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
24SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
25SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
26SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
27SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
28SERSER9SN9SN(chain B and (resid 3 through 12 or (resid 13...BB - F2 - 9002
31THRTHRPHEPHE(chain C and (resid 3 through 12 or (resid 13...CC3 - 123 - 12
32ARGARGARGARG(chain C and (resid 3 through 12 or (resid 13...CC1313
33SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
34SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
35SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
36SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
37SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
38SERSERPGEPGE(chain C and (resid 3 through 12 or (resid 13...CC - H2 - 9012
41THRTHRPROPRO(chain D and (resid 3 through 18 or resid 20...DD3 - 183 - 18
42THRTHRLEULEU(chain D and (resid 3 through 18 or resid 20...DD20 - 3020 - 30
43ARGARGCYSCYS(chain D and (resid 3 through 18 or resid 20...DD32 - 3532 - 35
44THRTHRARGARG(chain D and (resid 3 through 18 or resid 20...DD37 - 5537 - 55
45VALVALALAALA(chain D and (resid 3 through 18 or resid 20...DD57 - 6757 - 67
46LEULEUSERSER(chain D and (resid 3 through 18 or resid 20...DD69 - 8769 - 87
47ARGARGARGARG(chain D and (resid 3 through 18 or resid 20...DD8888
48THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
49THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
410THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
411THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
412THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
413THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003
414THRTHR9SN9SN(chain D and (resid 3 through 18 or resid 20...DD - I3 - 9003

-
Components

#1: Protein
Anthranilate--CoA ligase


Mass: 44395.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsA, PA0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X3, anthranilate-CoA ligase
#2: Chemical
ChemComp-9SN / 6-fluoroanthraniloyl-AMP


Mass: 484.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18FN6O8P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1444 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 tri-sodium citrate, 250 mM ammonium acetate, 27.9% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→46.023 Å / Num. obs: 188926 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 9.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.072 / Rrim(I) all: 0.171 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.67-1.750.8790.6340.4270.98198.9
9.15-46.025.40.060.9970.0280.06698

-
Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Coot0.8.8model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→46.023 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.35
RfactorNum. reflection% reflection
Rfree0.3132 9229 4.89 %
Rwork0.2695 --
obs0.2716 188879 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.68 Å2 / Biso mean: 22.2109 Å2 / Biso min: 0.81 Å2
Refinement stepCycle: final / Resolution: 1.67→46.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12019 0 228 1444 13691
Biso mean--15.67 22.2 -
Num. residues----1570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512609
X-RAY DIFFRACTIONf_angle_d0.77317201
X-RAY DIFFRACTIONf_chiral_restr0.0461865
X-RAY DIFFRACTIONf_plane_restr0.0052362
X-RAY DIFFRACTIONf_dihedral_angle_d16.2117568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8551X-RAY DIFFRACTION8.683TORSIONAL
12B8551X-RAY DIFFRACTION8.683TORSIONAL
13C8551X-RAY DIFFRACTION8.683TORSIONAL
14D8551X-RAY DIFFRACTION8.683TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.6890.35992840.31435913619799
1.689-1.70880.36053110.31745935624699
1.7088-1.72970.34233310.31055836616799
1.7297-1.75160.37462950.30786001629699
1.7516-1.77460.38572880.3075902619099
1.7746-1.79890.35453300.30195951628199
1.7989-1.82460.35582940.29815896619099
1.8246-1.85190.34822930.29325901619499
1.8519-1.88080.33252780.28556032631099
1.8808-1.91170.31223380.283659556293100
1.9117-1.94460.34543180.290459826300100
1.9446-1.980.36023150.286359656280100
1.98-2.01810.34343290.283159636292100
2.0181-2.05930.31452890.271360196308100
2.0593-2.1040.30923180.265360196337100
2.104-2.1530.30253190.262159746293100
2.153-2.20680.31432910.261560026293100
2.2068-2.26650.28952910.266360166307100
2.2665-2.33320.31583100.261559856295100
2.3332-2.40850.30373000.257960106310100
2.4085-2.49460.30073180.251559946312100
2.4946-2.59440.28243010.255460116312100
2.5944-2.71250.31043050.257560546359100
2.7125-2.85550.30723380.250859576295100
2.8555-3.03440.30142820.257560466328100
3.0344-3.26860.30022920.269260596351100
3.2686-3.59740.32243300.265560196349100
3.5974-4.11770.27253050.255760216326100
4.1177-5.18670.27782900.235461026392100
5.1867-46.0410.30133460.28536130647699
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)
10.84720.2983-0.26321.3871-0.11330.57320.01640.00450.03520.0726-0.02160.0975-0.0739-0.0901-0.00670.30230.0193-0.02110.2579-0.04450.116713.95285.71917.542
20.158-0.01820.03620.45960.04410.19070.01480.02740.0757-0.09290.0770.0344-0.139-0.1083-0.07390.41660.01750.01910.27050.01780.176416.4153-4.41535.7868
30.5013-0.2579-0.20430.94110.67450.60230.01110.0261-0.0029-0.0446-0.0193-0.06260.00040.04330.01640.4433-0.0544-0.01480.29430.03640.190116.5224-4.2616-4.5765
40.4329-0.03470.31360.5086-0.2362.313-0.04020.02090.0687-0.00160.02220.0594-0.1027-0.13110.01960.2312-0.0138-0.03170.20380.01290.16734.7833-5.100310.9303
50.13120.14670.35141.31530.52820.98710.072-0.028-0.001-0.0010.003-0.03850.01060.0695-0.05280.27680.0211-0.01490.195-0.00380.095125.7363-8.331217.3305
60.3304-0.0485-0.07410.24710.11370.1411-0.0045-0.00530.01940.0580.0057-0.0095-0.0646-0.0083-0.01750.3891-0.0062-0.03160.2194-0.01980.159426.71635.970316.2639
71.14670.4432-0.54320.3848-0.27020.27680.03250.1007-0.0008-0.20340.0008-0.11050.01120.0354-0.0240.36540.02180.04950.32430.06650.165229.55913.11634.5282
80.3461-0.22240.03170.4024-0.18260.33530.00330.06760.07060.086-0.0786-0.0341-0.16460.02310.02550.45510.00810.03170.20220.02330.123740.942913.373814.8752
91.10720.87590.2771.55250.32740.4292-0.0146-0.03380.07640.0801-0.0502-0.0297-0.04440.01130.04020.3805-0.0091-0.04440.1380.01870.130738.98541.898723.6443
100.0634-0.1542-0.09150.64690.26840.5323-0.00680.0328-0.00040.1482-0.0279-0.05560.06720.02730.01980.3451-0.01610.02350.1799-0.05980.134540.1391-11.79225.9359
111.09320.5217-0.04371.20940.60490.71560.04050.1064-0.0989-0.0274-0.0142-0.0816-0.02580.04450.02710.41510.0073-0.04970.2228-0.00210.122742.8596-11.504822.4402
120.2893-0.0407-0.07580.06310.04580.1072-0.0081-0.03050.069-0.02150.1166-0.0809-0.040.13050.0686-0.0649-0.01140.04740.0706-0.02950.121952.58511.533260.1937
130.33210.007-0.10670.17920.01680.2370.0778-0.06310.08840.05340.0717-0.0756-0.07310.13730.03940.0298-0.02110.03990.093-0.02420.106247.00424.116859.0031
140.28290.0025-0.16610.13070.00870.29410.1240.07930.15330.00720.01920.0401-0.1798-0.06290.13980.07010.00490.09360.05990.04650.009727.957811.295549.8431
150.65170.0060.11230.2359-0.00370.4033-0.02140.076-0.06-0.05180.03420.07690.0674-0.1583-0.00010.0839-0.03410.00520.1039-0.02980.070526.5142-9.651545.8126
160.81040.1371-0.11041.2096-0.23640.52360.0138-0.0014-0.17230.0051-0.004-0.08780.01240.0904-0.01910.38410.0501-0.02340.26080.00620.200122.976139.16912.4335
170.23590.1234-0.1210.69180.11650.2938-0.03730.11050.0378-0.07750.08820.0460.0395-0.0658-0.04880.3649-0.02820.00150.26890.05390.176814.806949.5593.6063
180.1762-0.17710.06570.4519-0.2030.49220.02820.1136-0.0428-0.1080.0436-0.01020.1445-0.0623-0.05120.3811-0.0319-0.00140.32860.03180.254724.36545.05931.94
190.36530.2655-0.12661.11880.04880.46460.1123-0.094-0.09710.01020.01980.03290.0541-0.0708-0.08820.4207-0.061-0.02430.27090.04760.15769.153242.572217.4478
200.88890.18630.30750.43730.39950.66170.10570.0843-0.2545-0.0757-0.06050.02080.14160.0034-0.02290.4752-0.0394-0.07840.23070.01620.21127.227231.31810.6253
210.65630.38590.19880.51580.04160.50270.1345-0.0398-0.1670.0302-0.0668-0.01250.2367-0.0577-0.02260.5085-0.0294-0.09920.2396-0.01950.1937-6.164131.402617.7834
220.77130.1085-0.08390.6891-0.17060.5879-0.0470.02640.0024-0.0364-0.13060.12110.1154-0.18610.13280.2941-0.04820.02620.2234-0.04870.157-5.817453.022924.2388
230.10540.00410.0466-0.00120.00260.03230.01660.0359-0.1526-0.01550.01750.0750.0666-0.0559-0.0191-0.0577-0.0517-0.07680.07510.03070.131845.445942.882657.0611
240.1229-0.0615-0.01940.27180.00080.0937-0.0431-0.0909-0.00360.08190.0743-0.05610.013-0.0203-0.0325-0.02020.0632-0.04220.02960.00290.061253.652653.128765.6479
250.1188-0.08830.06591.12730.27350.46920.0282-0.0797-0.06630.16370.0339-0.08550.0735-0.0308-0.07860.13170.04860.00170.1370.06670.161249.24647.655974.4856
260.2411-0.02110.020.1414-0.02460.24960.04740.1096-0.0398-0.00940.04260.09410.0612-0.0870.0564-0.0337-0.01-0.03380.05940.01610.09353.427546.370753.1179
270.270.0350.13590.1165-0.03070.08850.0514-0.0349-0.10280.0381-0.0228-0.01740.03990.01-0.04490.1134-0.0644-0.09670.05380.04490.203762.519631.68364.0153
280.1011-0.08540.01060.2426-0.10680.10060.10280.0103-0.1613-0.0165-0.03080.03460.1185-0.0145-0.0930.1332-0.0036-0.14370.0578-0.05560.144171.626331.358355.1923
290.3843-0.26850.00780.24350.07370.21920.10110.104-0.0857-0.00810.0158-0.05980.13190.16420.09130.09120.0781-0.02650.1351-0.07020.067675.132338.456747.7173
300.62410.2899-0.03661.01460.07460.3893-0.03540.20220.0459-0.09820.065-0.0626-0.0940.1626-0.04160.0838-0.01320.00380.21560.01940.063278.132856.233740.0258
310.6529-0.1675-0.33980.04540.1110.34980.00610.03210.1549-0.0153-0.0201-0.0259-0.08040.0932-0.06560.053-0.0161-0.00490.11010.07080.143865.287362.438550.003
321.4716-0.16590.17071.24810.05251.27720.04560.1174-0.0544-0.03580.021-0.1261-0.00750.2481-0.02240.0654-0.0160.01830.16170.03360.100478.918453.320945.3496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )A3 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 106 )A28 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 135 )A107 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 155 )A136 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 189 )A156 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 223 )A190 - 223
7X-RAY DIFFRACTION7chain 'A' and (resid 224 through 246 )A224 - 246
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 302 )A247 - 302
9X-RAY DIFFRACTION9chain 'A' and (resid 303 through 322 )A303 - 322
10X-RAY DIFFRACTION10chain 'A' and (resid 323 through 366 )A323 - 366
11X-RAY DIFFRACTION11chain 'A' and (resid 367 through 399 )A367 - 399
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 106 )B2 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 246 )B107 - 246
14X-RAY DIFFRACTION14chain 'B' and (resid 247 through 335 )B247 - 335
15X-RAY DIFFRACTION15chain 'B' and (resid 336 through 398 )B336 - 398
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 63 )C2 - 63
17X-RAY DIFFRACTION17chain 'C' and (resid 64 through 106 )C64 - 106
18X-RAY DIFFRACTION18chain 'C' and (resid 107 through 155 )C107 - 155
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 209 )C156 - 209
20X-RAY DIFFRACTION20chain 'C' and (resid 210 through 254 )C210 - 254
21X-RAY DIFFRACTION21chain 'C' and (resid 255 through 322 )C255 - 322
22X-RAY DIFFRACTION22chain 'C' and (resid 323 through 398 )C323 - 398
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 63 )D3 - 63
24X-RAY DIFFRACTION24chain 'D' and (resid 64 through 106 )D64 - 106
25X-RAY DIFFRACTION25chain 'D' and (resid 107 through 135 )D107 - 135
26X-RAY DIFFRACTION26chain 'D' and (resid 136 through 223 )D136 - 223
27X-RAY DIFFRACTION27chain 'D' and (resid 224 through 246 )D224 - 246
28X-RAY DIFFRACTION28chain 'D' and (resid 247 through 283 )D247 - 283
29X-RAY DIFFRACTION29chain 'D' and (resid 284 through 322 )D284 - 322
30X-RAY DIFFRACTION30chain 'D' and (resid 323 through 349 )D323 - 349
31X-RAY DIFFRACTION31chain 'D' and (resid 350 through 376 )D350 - 376
32X-RAY DIFFRACTION32chain 'D' and (resid 377 through 399 )D377 - 399

+
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