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- PDB-4q2u: Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 4q2u
TitleCrystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex
Components
  • Antitoxin DinJ
  • mRNA interferase YafQ
KeywordsTOXIN/TOXIN REPRESSOR / Bacterial Toxin-Antitoxin complex / Translation control / RHH motif / Ribonuclease / DNA binding / Ribosome binding / TOXIN-TOXIN REPRESSOR complex
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / toxic substance binding / cis-regulatory region sequence-specific DNA binding / translational termination / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters ...negative regulation of DNA-templated transcription initiation / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / toxic substance binding / cis-regulatory region sequence-specific DNA binding / translational termination / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome binding / Hydrolases; Acting on ester bonds / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / protein homodimerization activity / DNA binding / RNA binding
Similarity search - Function
Antitoxin DinJ / RelB antitoxin/Antitoxin DinJ / RelB antitoxin / Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix ...Antitoxin DinJ / RelB antitoxin/Antitoxin DinJ / RelB antitoxin / Toxin-antitoxin system, YafQ-like toxin / Bacterial toxin of type II toxin-antitoxin system, YafQ / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc-type ribbon-helix-helix / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA interferase toxin YafQ / Antitoxin DinJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMaehigashi, T. / Ruangprasert, A. / Dunham, C.M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanisms of Toxin Inhibition and Transcriptional Repression by Escherichia coli DinJ-YafQ.
Authors: Ruangprasert, A. / Maehigashi, T. / Miles, S.J. / Giridharan, N. / Liu, J.X. / Dunham, C.M.
History
DepositionApr 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin DinJ
B: mRNA interferase YafQ
C: Antitoxin DinJ
D: mRNA interferase YafQ
E: Antitoxin DinJ
F: mRNA interferase YafQ
G: Antitoxin DinJ
H: mRNA interferase YafQ
I: Antitoxin DinJ
J: mRNA interferase YafQ
K: Antitoxin DinJ
L: mRNA interferase YafQ
M: Antitoxin DinJ
N: mRNA interferase YafQ
O: Antitoxin DinJ
P: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,58165
Polymers173,87316
Non-polymers4,70749
Water20,5731142
1
A: Antitoxin DinJ
B: mRNA interferase YafQ
O: Antitoxin DinJ
P: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,71717
Polymers43,4684
Non-polymers1,24913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-233 kcal/mol
Surface area16850 Å2
MethodPISA
2
C: Antitoxin DinJ
D: mRNA interferase YafQ
K: Antitoxin DinJ
L: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62116
Polymers43,4684
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-254 kcal/mol
Surface area17250 Å2
MethodPISA
3
E: Antitoxin DinJ
F: mRNA interferase YafQ
I: Antitoxin DinJ
J: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,52515
Polymers43,4684
Non-polymers1,05711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-223 kcal/mol
Surface area16880 Å2
MethodPISA
4
G: Antitoxin DinJ
H: mRNA interferase YafQ
M: Antitoxin DinJ
N: mRNA interferase YafQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,71717
Polymers43,4684
Non-polymers1,24913
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-238 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.540, 120.920, 120.830
Angle α, β, γ (deg.)90.00, 130.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Antitoxin DinJ


Mass: 9512.576 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dinJ, b0226, JW0216 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47150
#2: Protein
mRNA interferase YafQ / Endoribonuclease YafQ / Toxin YafQ


Mass: 12221.604 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yafQ, b0225, JW0215 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q47149, Hydrolases; Acting on ester bonds
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.9-2.3M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 353442 / Num. obs: 353442 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.4 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.092
Reflection shellResolution: 1.76→1.82 Å / Rsym value: 0.614 / % possible all: 94.41

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Processing

Software
NameVersionClassification
SHELXDphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→43.906 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 3563 1.06 %
Rwork0.1781 --
obs0.1785 335490 95.66 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11137 0 245 1142 12524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511662
X-RAY DIFFRACTIONf_angle_d1.42415771
X-RAY DIFFRACTIONf_dihedral_angle_d10.8094408
X-RAY DIFFRACTIONf_chiral_restr0.0961743
X-RAY DIFFRACTIONf_plane_restr0.0081978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.35341150.321911781X-RAY DIFFRACTION86
1.8247-1.85070.37381480.310512806X-RAY DIFFRACTION92
1.8507-1.87840.30691350.294413196X-RAY DIFFRACTION94
1.8784-1.90770.28651480.282313157X-RAY DIFFRACTION96
1.9077-1.9390.28341380.275113416X-RAY DIFFRACTION96
1.939-1.97240.31671480.266313327X-RAY DIFFRACTION96
1.9724-2.00830.24111540.249313404X-RAY DIFFRACTION97
2.0083-2.04690.28311410.230213431X-RAY DIFFRACTION97
2.0469-2.08870.25631370.215113390X-RAY DIFFRACTION97
2.0887-2.13410.24691510.202613436X-RAY DIFFRACTION97
2.1341-2.18370.20571380.186113503X-RAY DIFFRACTION97
2.1837-2.23840.21461550.184513518X-RAY DIFFRACTION97
2.2384-2.29890.2041390.175213434X-RAY DIFFRACTION97
2.2989-2.36650.23381590.178913448X-RAY DIFFRACTION97
2.3665-2.44290.22481300.179513486X-RAY DIFFRACTION97
2.4429-2.53020.22621570.173913405X-RAY DIFFRACTION97
2.5302-2.63150.22121270.165513520X-RAY DIFFRACTION97
2.6315-2.75120.2591560.164213444X-RAY DIFFRACTION97
2.7512-2.89630.17281380.159213438X-RAY DIFFRACTION97
2.8963-3.07770.21021350.156313330X-RAY DIFFRACTION97
3.0777-3.31520.21081550.160313345X-RAY DIFFRACTION96
3.3152-3.64870.17751470.140113313X-RAY DIFFRACTION96
3.6487-4.17630.13311460.129813202X-RAY DIFFRACTION95
4.1763-5.26030.18431350.136212985X-RAY DIFFRACTION93
5.2603-43.91870.21741310.186813212X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.03260.11130.03110.20610.10220.1487-0.22430.0564-0.22880.2890.10820.133-0.14250.0924-00.16810.02520.02060.17290.00110.159121.4378114.917416.7113
20.12020.077-0.05910.1790.13420.0762-0.0793-0.18360.16520.180.0977-0.0634-0.14130.1023-00.16280.0065-0.00690.1832-0.02570.206536.3291119.128113.2355
3-0.1092-0.0258-0.26280.31410.33380.22490.0327-0.00740.06620.02410.0422-0.09630.01490.072300.14010.0231-0.00990.136-0.0210.149830.4248106.9867-0.312
40.0998-0.027-0.06750.00020.05590.0512-0.1240.2545-0.292-0.08240.0932-0.17580.03770.0743-0.00070.22350.0007-0.01090.2167-0.01550.152336.954586.0786-18.8865
50.05340.0207-0.02210.0159-0.00860.02610.22030.435-0.3861-0.185-0.04560.23820.2197-0.32280.0250.27220.0123-0.06450.2051-0.04560.204226.123286.82-21.6857
6-0.0031-0.00260.02240.0770.04590.06820.18570.3535-0.2681-0.1093-0.1147-0.0891-0.05010.26320.00070.18640.0427-00.2615-0.03290.13636.513692.5452-21.5207
70.0371-0.04980.04240.037-0.04320.01790.0573-0.02340.00910.0358-0.0379-0.01360.1223-0.0351-00.1536-0.0058-0.01380.1147-0.00020.157925.57487.649-9.1499
80.0362-0.14670.05130.1930.00540.1411-0.0443-0.02690.0199-0.0570.09630.11410.1326-0.07690.0030.1360.0123-0.03010.2001-0.00350.13621.60495.8199-15.8619
90.0289-0.0050.04720.0350.00330.0389-0.03020.05960.1106-0.2218-0.0875-0.0149-0.1438-0.1159-00.17420.0187-0.00030.15590.00820.182728.4846106.5258-20.9373
100.11190.1394-0.09380.26170.0020.34080.0579-0.09520.00020.1882-0.0315-0.1682-0.28330.13570.07670.1241-0.0243-0.03320.1649-0.01830.182537.5835104.7503-8.6174
110.1061-0.01090.10710.25160.15180.08060.0098-0.16610.0290.0584-0.0604-0.0041-0.0108-0.0478-0.03070.0860.0218-0.00830.126-0.01450.113729.589101.0937-10.8477
120.30970.05690.34360.39170.13740.27190.010.028-0.02830.0321-0.0209-0.0590.059-0.007600.11270.013-0.01430.13060.0010.114433.623696.7205-10.6366
130.16070.0951-0.04180.23540.14910.09290.0283-0.0657-0.10160.10280.07090.26540.0143-0.1204-0.00940.17080.03280.02480.21240.04150.143-8.360385.151970.4587
140.04370.0353-0.03390.08380.02960.0161-0.00680.1847-0.07320.00530.04530.15380.1224-0.146100.202-0.024-0.01130.17230.00310.1804-6.703780.737955.6159
150.09270.2984-0.18070.31490.04740.139-0.03920.04850.0454-0.06590.02510.06840.0671-0.0079-0.00450.1208-0.0081-0.01110.1390.02650.13937.105893.418259.2385
160.03430.03-0.03430.0374-0.02010.0606-0.08630.1580.1021-0.09540.0566-0.1053-0.38010.2078-00.1814-0.0463-0.0270.20520.01790.212823.6447114.737950.095
170.0116-0.024-0.00840.01620.01790.0181-0.1509-0.08480.20130.0561-0.0744-0.2234-0.43970.426700.2065-0.0679-0.05770.25380.00980.29127.9248114.400160.4806
180.72670.0121-0.03720.2946-0.14620.296-0.24750.38630.013-0.0373-0.0743-0.104-0.21980.4324-0.04660.1359-0.0340.00150.34120.03610.177726.206108.502650.2145
190.0229-0.0167-0.02050.0449-0.03590.03180.01840.00780.14560.02330.0158-0.0142-0.09470.0222-00.15810.0028-0.01980.14980.00190.160615.5963113.150362.6202
200.1116-0.09460.10130.177-0.09460.1858-0.1049-0.10160.13290.21530.1242-0.08210.013-0.01580.02960.1460.0208-0.04170.23740.02210.151323.8003105.174965.6874
210.0457-0.00560.04130.0367-0.03050.00960.0726-0.1299-0.1692-0.2014-0.1399-0.10680.32710.325300.21510.05680.00270.2130.03770.211927.854594.717358.7702
220.2375-0.16140.03510.14330.0390.3069-0.0566-0.1016-0.2954-0.28930.09430.14510.1643-0.3974-0.00450.182-0.025-0.03610.1778-0.00560.154514.32295.55651.2679
230.0065-0.0503-0.02160.2080.01760.00740.0483-0.1101-0.00990.039-0.03390.06780.0481-0.0584-00.1233-0.0103-0.01670.16550.02880.12817.417799.587758.8159
240.158-0.01990.24890.1792-0.05740.2889-0.0294-0.014-0.0172-0.0359-0.02790.05640.0410.0581-0.00060.1094-0.01-0.00790.15030.02540.140916.487103.776354.7471
250.26380.0596-0.15640.14240.04930.07750.0889-0.00790.0587-0.01230.05780.0143-0.21730.1158-00.23450.0096-0.00240.16870.02860.17999.3669127.330930.3463
260.17370.0183-0.21720.1565-0.11580.11010.0307-0.03720.13220.1291-0.1409-0.1586-0.09970.1551-0.00050.1395-0.01060.00240.19590.02280.18618.8754115.185132.8906
270.34620.3162-0.1810.5054-0.0044-0.04770.0153-0.043-0.034-0.0115-0.0556-0.07890.00080.00330.00010.1404-0.0192-0.00890.1410.01890.13150.8979108.426233.8365
280.0621-0.0207-0.02630.1476-0.06470.03860.01020.0056-0.00420.1235-0.00790.20140.0358-0.055100.2012-0.02680.0040.234-0.0020.2014-17.643590.108145.0429
290.0141-0.0054-0.02460.01530.0080.01240.0689-0.1238-0.1258-0.1913-0.19540.4076-0.0199-0.4446-0.00090.1507-0.0262-0.02190.287-0.02640.2249-24.902794.737137.658
300.0653-0.0690.04440.0333-0.06970.08050.038-0.1756-0.2499-0.01370.168-0.13880.125-0.18840.00030.1733-0.0537-0.02150.18280.00150.2018-14.920988.35838.8408
310.0051-0.0747-0.01630.03730.06410.05780.0032-0.07990.00310.0759-0.08450.1186-0.012-0.188-0.00040.10190.0108-0.00820.1626-0.01590.1298-18.6902104.839642.1182
320.08310.1131-0.05880.1745-0.14690.2618-0.0017-0.05990.07290.0612-0.0271-0.0108-0.0264-0.2412-0.02990.15670.0084-0.04690.1860.00220.1543-19.0133101.444530.6654
330.03210.0147-0.03180.02290.04650.0665-0.23160.11920.0132-0.33550.08420.11670.18170.038-00.1940.0023-0.00510.17030.00650.1431-10.488193.774624.3297
340.21060.0792-0.07170.32090.2350.17250.00170.0066-0.1343-0.0090.0515-0.0079-0.10970.43910.00320.10630.0003-0.00730.17650.01420.1667-0.226497.748335.2121
350.1509-0.0317-0.13060.02040.10740.16620.00120.050.07640.0003-0.0683-0.0068-0.00690.0577-0.03370.1197-0.0101-0.0310.1250.01640.1303-8.4199101.003233.1552
360.2477-0.03410.1450.0782-0.0710.2760.0363-0.0094-0.02740.0379-0.04630.01530.0301-0.02430.0010.1263-0.028-0.00680.1150.01960.1352-8.732798.606838.6114
370.07410.1495-0.05110.20410.01370.2586-0.08170.2101-0.2079-0.02870.0776-0.02070.04680.059700.17040.0177-0.02160.1734-0.01760.250158.397672.5588-7.567
380.02570.0323-0.08550.0906-0.0190.1051-0.04320.307-0.1431-0.2331-0.04330.06950.036-0.0176-0.00230.19660.029-0.00310.2098-0.00210.139754.789385.1308-16.3269
390.0941-0.08910.00830.01430.00380.0589-0.05730.1466-0.0525-0.04180.0182-0.0273-0.12790.293-00.17320.01690.00840.159-0.01050.166466.337783.7155-5.3556
400.00930.05930.05650.0750.0980.08890.04270.1649-0.0521-0.0866-0.10520.00720.0143-0.016100.16870.0108-0.01720.1711-0.03620.166756.687591.42482.6052
410.1376-0.0707-0.07990.04080.06540.10740.15060.063-0.0703-0.0561-0.22820.2493-0.0417-0.17820.01770.10630.0278-0.01980.1703-0.02850.166743.149100.713410.2038
420.0537-0.05720.12920.2345-0.20470.2322-0.1326-0.2545-0.00730.19540.18370.1539-0.2567-0.28820.05610.18130.0393-0.01170.2037-0.08190.159647.4276108.953921.8331
430.29570.1798-0.17020.1913-0.10530.0831-0.0828-0.74270.02390.34160.0807-0.31920.0045-0.0318-0.00270.22550.0187-0.03010.3184-0.05210.153155.7965103.584728.5452
440.04690.00720.0460.0127-0.03740.0424-0.1025-0.19430.30880.07150.0130.0617-0.2249-0.072500.19270.0102-0.03380.187-0.02810.226853.9572110.857618.8985
450.0734-0.0441-0.02230.0471-0.02170.01330.15-0.31140.03480.1164-0.08020.11790.0159-0.118700.1517-0.0088-0.02270.17870.0110.148650.338594.030222.3789
460.17610.0221-0.03780.05620.07870.23020.0346-0.1112-0.0954-0.0287-0.0209-0.01240.04980.0434-0.00550.11360.0125-0.04920.1703-0.01890.155561.726696.887921.613
470.0945-0.02490.08930.02510.01870.0460.0825-0.00080.11690.09160.1207-0.4534-0.07960.2613-00.14760.0151-0.0010.191-0.02030.212667.5372104.867212.7189
480.07830.0235-0.17870.0182-0.06180.22120.00810.37810.0195-0.26660.02830.0411-0.1418-0.02800.16970.0142-0.03030.17620.01050.163655.3399102.0443.6462
490.1616-0.0116-0.18450.0302-0.08070.19310.03880.00810.0193-0.04550.0247-0.00340.07230.04330.0650.10160.0191-0.02090.117-0.02410.126158.249698.214511.3432
500.233-0.1044-0.10010.0583-0.06410.1765-0.01620.0390.01010.05280.0383-0.00040.00940.0156-0.00020.10420.009-0.0360.1073-0.02250.161253.0549100.760312.4534
510.06820.0203-0.07340.2055-0.02470.0576-0.04970.0671-0.0935-0.10870.3368-0.3123-0.38880.20950.00130.2982-0.0334-0.00640.18410.00960.18511.8824127.416629.9166
520.1201-0.0998-0.08160.14470.13510.0970.04770.02520.0251-0.1018-0.03580.0829-0.1694-0.16170.00020.16330.0386-0.02010.1678-0.0010.1859-2.6369122.191826.063
530.0622-0.020.0034-0.01790.00040.0654-0.01070.0776-0.05010.1685-0.10390.0996-0.05930.082800.14570.00130.00510.1351-0.00440.15567.9264114.567435.3986
540.2626-0.2495-0.15260.2764-0.00740.13940.00390.07230.0643-0.02920.01870.02950.0075-0.189100.2093-0.02330.00440.17680.00570.13969.6796102.200215.5985
550.46350.03880.17130.0523-0.04540.1147-0.34120.5042-0.437-0.14690.0252-0.26510.41420.1862-0.04720.55470.00010.11520.2233-0.04580.343414.564983.97097.8802
560.0175-0.00110.00460.02320.02450.0196-0.10730.0739-0.3326-0.20590.0195-0.61280.15720.209-0.06490.43010.15820.14490.3228-0.00720.445123.227182.146315.7239
570.2393-0.07580.14920.0412-0.0540.1201-0.10570.2287-0.16180.3051-0.02910.17330.3597-0.0741-0.03340.4928-0.06630.12730.1656-0.05730.35511.649382.332314.3471
580.08580.0089-0.03280.0456-0.04820.063-0.1359-0.0531-0.0895-0.1435-0.1644-0.10250.28560.2839-0.01140.2580.07580.07680.3030.06640.228823.697794.521613.3065
590.0819-0.0447-0.09590.00210.00710.5118-0.1233-0.0274-0.10230.0096-0.0442-0.26770.46730.73620.02720.27170.05170.0510.31380.11260.300521.866989.780724.1444
600.48310.31190.32160.29220.25750.219-0.1197-0.1997-0.09560.1974-0.17120.04810.5512-0.1898-0.07710.4427-0.00880.07070.20470.03650.217710.586987.103529.8277
610.1237-0.071-0.14940.1001-0.00050.1011-0.02360.0685-0.09030.18320.08350.30850.0348-0.286700.1427-0.0173-0.00910.20070.01480.14734.114897.520120.1673
620.1354-0.0764-0.23910.1937-0.0590.4524-0.1191-0.016-0.0571-0.00230.0741-0.10970.1190.1018-0.00280.1904-0.01090.03040.14950.01190.167812.29294.893919.3193
630.00550.04670.05770.04210.10880.26330.21240.3927-0.034-0.1206-0.2202-0.23360.29610.61890.03960.3270.02070.20850.43940.02490.431829.313373.332642.7298
640.00230.0172-0.00720.05520.00390.049-0.0113-0.0854-0.1428-0.37720.0981-0.09020.76840.053300.4263-0.00410.01570.199-0.01120.269814.62763.458946.3801
650.0694-0.12880.10580.1591-0.09550.13210.14360.2919-0.0641-0.69270.01170.08490.4828-0.03030.00020.4605-0.03560.01330.32220.02190.229313.140872.657939.0788
660.73950.19560.17390.16040.18260.23060.06660.12580.584-0.5947-0.1675-0.3094-0.036-0.0334-0.0620.35480.04570.1260.27730.08150.281318.271284.476540.4918
670.01190.0160.01710.08490.03760.03680.0479-0.28160.02530.12390.1410.039-0.286-0.0155-00.2139-0.015-0.02090.21660.03050.223319.519181.26255.724
680.0795-0.0827-0.06870.2433-0.11570.1294-0.05930.0926-0.0847-0.10110.0208-0.0211-0.052-0.1664-00.18120.00330.01720.17710.00650.18615.149277.155948.8761
690.1787-0.15490.27790.2610.01460.4030.0126-0.0281-0.0505-0.1376-0.0415-0.14370.05890.111800.2078-0.00880.05290.16460.01290.267319.047473.358951.2223
700.1402-0.0563-0.16020.10310.08020.1293-0.0337-0.0416-0.21570.2363-0.1741-0.03940.0114-0.219-0.01010.2303-0.0120.00920.22180.04860.2428-8.875782.698970.0284
710.1597-0.0067-0.07110.07860.10230.1008-0.0192-0.1574-0.00240.16280.07440.06690.03830.208600.20630.00320.02040.2339-0.01740.13333.894789.905374.6669
720.07580.1023-0.03970.55140.20640.28790.0050.0339-0.01620.0339-0.048-0.03160.0280.0139-0.04090.1180.00480.01290.12090.03780.13488.283980.775158.8041
730.43530.18380.20890.1617-0.00170.2660.23430.3993-0.5175-0.5240.2927-0.664-0.0256-0.04450.1420.45790.12270.22380.42650.00840.524229.189565.340245.8272
740.00460.02250.01160.0138-0.00960.0275-0.04170.5011-0.3197-0.481-0.0491-0.05830.1154-0.018700.57060.07820.10490.3822-0.08360.311121.63765.588536.43
750.03540.0071-0.07890.16060.01880.0772-0.05820.1237-0.3912-0.23620.0955-0.04820.040.065200.20020.01590.01950.1793-0.03510.242859.997572.9367-9.9686
760.00390.1073-0.07560.1965-0.01520.1422-0.1044-0.2451-0.19220.1093-0.0248-0.17560.03610.2036-00.23260.0162-0.00910.15530.03270.209564.304277.53283.8446
770.0261-0.03110.09910.07640.14480.18430.02270.0506-0.01420.19440.01380.109-0.1072-0.01350.00010.11720.0017-0.00120.0987-0.00960.1253.648885.4578-5.1515
780.03050.0598-0.02150.0229-0.0640.0047-0.1688-0.10290.2405-0.0730.14840.0098-0.05280.013800.1912-0.00940.02140.192-0.00640.207265.38493.6757-8.1086
790.009-0.0015-0.02720.0487-0.00210.04750.0382-0.24980.04030.01530.0096-0.41110.02310.328300.1596-0.04460.03250.2476-0.05280.26981.3338101.6858-10.1558
800.0329-0.01770.01950.04850.03470.1317-0.04420.22430.2674-0.12350.2128-0.0341-0.65050.4430.00310.4656-0.13280.11380.33670.00140.586480.7264115.9242-14.2501
81-0.0039-0.01350.00570.0097-0.00570.0418-0.02230.48030.2367-0.45020.068-0.0944-0.451-0.09770.0010.6782-0.00550.1270.35150.10460.433471.6735118.1759-21.7978
820.043-0.08330.05330.1546-0.10890.08850.0555-0.03080.59680.0641-0.2087-0.1373-0.11680.2945-0.19810.449-0.3230.2325-0.5979-0.07340.499175.0084116.9204-10.6935
830.04410.0333-0.04210.02810.02670.05890.24810.3938-0.0354-0.2314-0.0204-0.1011-0.21590.3553-00.29810.01980.07550.31170.02940.223173.7958105.8834-23.0168
840.6057-0.1942-0.22290.0720.01550.17570.32190.83010.3738-0.2405-0.12110.0041-0.4066-0.35170.02680.33520.10380.07350.29670.05120.30163.3702110.6033-19.604
850.37320.13580.66410.3514-0.00821.40030.5361-0.21730.8160.1849-0.00540.3928-0.1644-0.46180.16250.27870.01020.13250.2003-0.04150.473459.2501112.9275-7.5343
860.06010.0039-0.11080.0479-0.06770.1329-0.041-0.0593-0.05790.15690.05570.10570.06970.1515-00.19970.0106-0.00550.2243-0.02770.179169.5062102.172-2.8152
870.115-0.0447-0.17070.1381-0.06210.17140.01610.13240.0758-0.20240.1346-0.0188-0.1283-0.12750.01890.2111-0.00250.02380.1842-0.01020.210666.379104.5142-10.997
880.26270.0335-0.0750.1553-0.24810.2860.00740.09150.16570.08360.0210.04-0.09270.054300.2397-0.03180.05050.191-0.03250.230672.2122105.6805-10.7894
890.10810.0756-0.11480.11080.0240.0850.0319-0.1933-0.0050.1565-0.05040.1623-0.1866-0.1215-00.20880.0220.00760.22560.00170.222822.1878117.487217.0944
900.08070.1487-0.05290.1507-0.09190.144-0.15520.00290.0450.04720.24230.0888-0.0379-0.145100.1314-0.01970.00890.1930.00070.155815.9408110.30255.1359
910.1213-0.1039-0.15950.26120.00440.18380.0144-0.00860.0226-0.1224-0.0215-0.00590.0539-0.0030.00030.14420.0044-0.00670.11590.0050.122931.0349119.7223-1.728
920.12050.03350.06340.16330.14130.2197-0.28960.01370.1726-0.83380.1104-0.376-0.56760.5208-0.05330.5840.02250.18540.37060.07620.385441.2619135.2216-23.4222
930.01550.02150.02330.03270.02910.0337-0.05610.0446-0.08130.03280.1298-0.479-0.32640.58050.00350.4019-0.10590.16720.36660.01120.543851.5978134.8451-17.192
940.2218-0.01250.0794-0.0046-0.00550.065-0.0570.31720.1149-0.4594-0.062-0.31580.09220.0504-0.13810.52360.03520.20630.32130.02310.270243.9898128.2907-23.446
950.0146-0.03170.02620.037-0.01050.0538-0.1102-0.00810.4453-0.10690.056-0.4394-0.1783-0.0920.01150.2772-0.01960.01110.1649-0.0250.414142.6738137.0333-8.5139
960.1251-0.20380.09820.2159-0.090.05690.006-0.01470.29730.00290.1435-0.6584-0.14320.1569-0.02390.24070.00670.05370.2576-0.05950.421149.7055128.0804-7.95
97-0.0084-0.0073-0.01620.0179-0.03170.00570.16870.0392-0.071-0.37670.0652-0.4780.32840.110700.37110.03660.10180.24560.01070.336948.2325115.9478-13.5691
980.08090.1149-0.0540.1186-0.00480.03980.03590.0682-0.2393-0.0947-0.03740.19190.1263-0.0727-00.1822-0.0141-0.0120.1557-0.01410.221632.8942118.9912-12.8657
990.134-0.0682-0.04410.29970.00280.01840.014-0.1957-0.0139-0.0461-0.0168-0.1797-0.1370.11390.00020.1955-0.00140.02540.1790.00020.210140.1913123.1106-9.3254
1000.17080.0355-0.0160.1469-0.10710.0781-0.05830.20050.1017-0.20280.0053-0.12290.014-0.0088-0.02050.29880.00070.07490.16290.01140.208439.6066126.3364-18.7555
1010.0066-0.00650.00080.00250.00850.0043-0.1235-0.3516-0.04460.089-0.0750.0342-0.1034-0.149800.2013-0.00870.02720.1706-0.03380.206533.7566127.7296-2.6437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:12)
2X-RAY DIFFRACTION2chain 'A' and (resseq 13:29)
3X-RAY DIFFRACTION3chain 'A' and (resseq 30:67)
4X-RAY DIFFRACTION4chain 'A' and (resseq 68:76)
5X-RAY DIFFRACTION5chain 'A' and (resseq 77:86)
6X-RAY DIFFRACTION6chain 'B' and (resseq 3:9)
7X-RAY DIFFRACTION7chain 'B' and (resseq 10:21)
8X-RAY DIFFRACTION8chain 'B' and (resseq 22:37)
9X-RAY DIFFRACTION9chain 'B' and (resseq 38:47)
10X-RAY DIFFRACTION10chain 'B' and (resseq 48:58)
11X-RAY DIFFRACTION11chain 'B' and (resseq 59:74)
12X-RAY DIFFRACTION12chain 'B' and (resseq 75:92)
13X-RAY DIFFRACTION13chain 'C' and (resseq 3:12)
14X-RAY DIFFRACTION14chain 'C' and (resseq 13:29)
15X-RAY DIFFRACTION15chain 'C' and (resseq 30:67)
16X-RAY DIFFRACTION16chain 'C' and (resseq 68:76)
17X-RAY DIFFRACTION17chain 'C' and (resseq 77:86)
18X-RAY DIFFRACTION18chain 'D' and (resseq 3:9)
19X-RAY DIFFRACTION19chain 'D' and (resseq 10:21)
20X-RAY DIFFRACTION20chain 'D' and (resseq 22:37)
21X-RAY DIFFRACTION21chain 'D' and (resseq 38:47)
22X-RAY DIFFRACTION22chain 'D' and (resseq 48:58)
23X-RAY DIFFRACTION23chain 'D' and (resseq 59:74)
24X-RAY DIFFRACTION24chain 'D' and (resseq 75:92)
25X-RAY DIFFRACTION25chain 'E' and (resseq 3:12)
26X-RAY DIFFRACTION26chain 'E' and (resseq 13:29)
27X-RAY DIFFRACTION27chain 'E' and (resseq 30:67)
28X-RAY DIFFRACTION28chain 'E' and (resseq 68:76)
29X-RAY DIFFRACTION29chain 'E' and (resseq 77:86)
30X-RAY DIFFRACTION30chain 'F' and (resseq 3:9)
31X-RAY DIFFRACTION31chain 'F' and (resseq 10:21)
32X-RAY DIFFRACTION32chain 'F' and (resseq 22:37)
33X-RAY DIFFRACTION33chain 'F' and (resseq 38:47)
34X-RAY DIFFRACTION34chain 'F' and (resseq 48:58)
35X-RAY DIFFRACTION35chain 'F' and (resseq 59:74)
36X-RAY DIFFRACTION36chain 'F' and (resseq 75:92)
37X-RAY DIFFRACTION37chain 'G' and (resseq 3:12)
38X-RAY DIFFRACTION38chain 'G' and (resseq 13:29)
39X-RAY DIFFRACTION39chain 'G' and (resseq 30:44)
40X-RAY DIFFRACTION40chain 'G' and (resseq 45:55)
41X-RAY DIFFRACTION41chain 'G' and (resseq 56:66)
42X-RAY DIFFRACTION42chain 'G' and (resseq 67:76)
43X-RAY DIFFRACTION43chain 'G' and (resseq 77:86)
44X-RAY DIFFRACTION44chain 'H' and (resseq 3:9)
45X-RAY DIFFRACTION45chain 'H' and (resseq 10:21)
46X-RAY DIFFRACTION46chain 'H' and (resseq 22:37)
47X-RAY DIFFRACTION47chain 'H' and (resseq 38:47)
48X-RAY DIFFRACTION48chain 'H' and (resseq 48:58)
49X-RAY DIFFRACTION49chain 'H' and (resseq 59:74)
50X-RAY DIFFRACTION50chain 'H' and (resseq 75:92)
51X-RAY DIFFRACTION51chain 'I' and (resseq 3:12)
52X-RAY DIFFRACTION52chain 'I' and (resseq 13:29)
53X-RAY DIFFRACTION53chain 'I' and (resseq 30:44)
54X-RAY DIFFRACTION54chain 'I' and (resseq 45:66)
55X-RAY DIFFRACTION55chain 'I' and (resseq 67:76)
56X-RAY DIFFRACTION56chain 'I' and (resseq 77:86)
57X-RAY DIFFRACTION57chain 'J' and (resseq 3:9)
58X-RAY DIFFRACTION58chain 'J' and (resseq 10:21)
59X-RAY DIFFRACTION59chain 'J' and (resseq 22:37)
60X-RAY DIFFRACTION60chain 'J' and (resseq 38:47)
61X-RAY DIFFRACTION61chain 'J' and (resseq 48:58)
62X-RAY DIFFRACTION62chain 'J' and (resseq 59:92)
63X-RAY DIFFRACTION63chain 'L' and (resseq 2:9)
64X-RAY DIFFRACTION64chain 'L' and (resseq 10:21)
65X-RAY DIFFRACTION65chain 'L' and (resseq 22:37)
66X-RAY DIFFRACTION66chain 'L' and (resseq 38:47)
67X-RAY DIFFRACTION67chain 'L' and (resseq 48:58)
68X-RAY DIFFRACTION68chain 'L' and (resseq 59:74)
69X-RAY DIFFRACTION69chain 'L' and (resseq 75:92)
70X-RAY DIFFRACTION70chain 'K' and (resseq 4:12)
71X-RAY DIFFRACTION71chain 'K' and (resseq 13:29)
72X-RAY DIFFRACTION72chain 'K' and (resseq 30:66)
73X-RAY DIFFRACTION73chain 'K' and (resseq 67:76)
74X-RAY DIFFRACTION74chain 'K' and (resseq 77:86)
75X-RAY DIFFRACTION75chain 'M' and (resseq 4:12)
76X-RAY DIFFRACTION76chain 'M' and (resseq 13:29)
77X-RAY DIFFRACTION77chain 'M' and (resseq 30:44)
78X-RAY DIFFRACTION78chain 'M' and (resseq 45:55)
79X-RAY DIFFRACTION79chain 'M' and (resseq 56:66)
80X-RAY DIFFRACTION80chain 'M' and (resseq 67:76)
81X-RAY DIFFRACTION81chain 'M' and (resseq 77:86)
82X-RAY DIFFRACTION82chain 'N' and (resseq 3:9)
83X-RAY DIFFRACTION83chain 'N' and (resseq 10:21)
84X-RAY DIFFRACTION84chain 'N' and (resseq 22:37)
85X-RAY DIFFRACTION85chain 'N' and (resseq 38:47)
86X-RAY DIFFRACTION86chain 'N' and (resseq 48:58)
87X-RAY DIFFRACTION87chain 'N' and (resseq 59:74)
88X-RAY DIFFRACTION88chain 'N' and (resseq 75:92)
89X-RAY DIFFRACTION89chain 'O' and (resseq 4:12)
90X-RAY DIFFRACTION90chain 'O' and (resseq 13:29)
91X-RAY DIFFRACTION91chain 'O' and (resseq 30:66)
92X-RAY DIFFRACTION92chain 'O' and (resseq 67:76)
93X-RAY DIFFRACTION93chain 'O' and (resseq 77:86)
94X-RAY DIFFRACTION94chain 'P' and (resseq 3:9)
95X-RAY DIFFRACTION95chain 'P' and (resseq 10:21)
96X-RAY DIFFRACTION96chain 'P' and (resseq 22:37)
97X-RAY DIFFRACTION97chain 'P' and (resseq 38:47)
98X-RAY DIFFRACTION98chain 'P' and (resseq 48:58)
99X-RAY DIFFRACTION99chain 'P' and (resseq 59:74)
100X-RAY DIFFRACTION100chain 'P' and (resseq 75:85)
101X-RAY DIFFRACTION101chain 'P' and (resseq 86:92)

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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