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- PDB-2a6q: Crystal structure of YefM-YoeB complex -

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Basic information

Entry
Database: PDB / ID: 2a6q
TitleCrystal structure of YefM-YoeB complex
Components
  • Antitoxin yefM
  • Toxin yoeB
KeywordsTOXIN INHIBITOR/TOXIN / YoeB / YefM / toxin / antitoxin / addiction modules / RNase / inhibitor / TOXIN INHIBITOR-TOXIN COMPLEX
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / toxic substance binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / toxic substance binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / response to heat / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like / YaeB-like fold ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #330 / YefM-like domain / Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Antitoxin YefM / Toxin YoeB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsKamada, K. / Hanaoka, F.
CitationJournal: Mol.Cell / Year: 2005
Title: Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin
Authors: Kamada, K. / Hanaoka, F.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin yefM
B: Antitoxin yefM
C: Antitoxin yefM
D: Antitoxin yefM
E: Toxin yoeB
F: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)58,9116
Polymers58,9116
Non-polymers00
Water2,756153
1
A: Antitoxin yefM
B: Antitoxin yefM
E: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)29,4553
Polymers29,4553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-51 kcal/mol
Surface area11890 Å2
MethodPISA
2
C: Antitoxin yefM
D: Antitoxin yefM
F: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)29,4553
Polymers29,4553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-47 kcal/mol
Surface area11450 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15520 Å2
ΔGint-108 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.485, 88.485, 135.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Detailstwo complexes of YoeB-YefM2 hetero-trimers in the asymmetric unit

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Components

#1: Protein
Antitoxin yefM


Mass: 9610.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yefM / Plasmid: modified pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69346
#2: Protein Toxin yoeB


Mass: 10233.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yoeB / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69348
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris-HCl, NaCl, DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.98020, 0.98000, 0.97020, 0.98430
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDNov 21, 2003rhodium-coated horizontal mirror
MARRESEARCH2CCDNov 21, 2003rhodium-coated horizontal mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1rotated-inclined double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2rotated-inclined double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98021
30.981
40.97021
50.98431
Reflection

Number: 104941 / Rmerge(I) obs: 0.037 / Χ2: 0.565 / D res high: 2.3 Å / D res low: 50 Å / % possible obs: 99.7 / Redundancy: 2.9 %

ID
1
2
3
4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955097.710.0190.6282.9
3.934.9510010.0240.7773
3.443.9310010.0310.6763
3.123.4410010.0480.5972.9
2.93.1210010.0760.562.9
2.732.910010.1170.5172.9
2.592.7310010.1740.5062.9
2.482.5910010.2460.4822.9
2.382.4810010.3330.4672.9
2.32.3899.710.4750.4332.9
4.955097.720.0190.6282.9
3.934.9510020.0240.7773
3.443.9310020.0310.6763
3.123.4410020.0480.5972.9
2.93.1210020.0760.562.9
2.732.910020.1170.5172.9
2.592.7310020.1740.5062.9
2.482.5910020.2460.4822.9
2.382.4810020.3330.4672.9
2.32.3899.720.4750.4332.9
4.955097.730.0190.6282.9
3.934.9510030.0240.7773
3.443.9310030.0310.6763
3.123.4410030.0480.5972.9
2.93.1210030.0760.562.9
2.732.910030.1170.5172.9
2.592.7310030.1740.5062.9
2.482.5910030.2460.4822.9
2.382.4810030.3330.4672.9
2.32.3899.730.4750.4332.9
4.955097.740.0190.6282.9
3.934.9510040.0240.7773
3.443.9310040.0310.6763
3.123.4410040.0480.5972.9
2.93.1210040.0760.562.9
2.732.910040.1170.5172.9
2.592.7310040.1740.5062.9
2.482.5910040.2460.4822.9
2.382.4810040.3330.4672.9
2.32.3899.740.4750.4332.9
ReflectionResolution: 2.03→44.28 Å / Num. all: 38671 / Num. obs: 38636 / % possible obs: 99.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 35.4 Å2 / Χ2: 0.565 / Net I/σ(I): 27.86
Reflection shellResolution: 2.02→2.09 Å / % possible obs: 99.7 % / Redundancy: 7.1 % / Num. measured obs: 10499 / Num. unique all: 3278 / Χ2: 0.433 / % possible all: 84.2

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.3 Å / D res low: 44.28 Å
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDR cullis acentricLoc acentricPower acentricReflection acentric
12.050.1052312
20.995.40.1352281
30.87.91.2452302
40.826.91.1352310
Phasing MAD set shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDResolution (Å)R cullis acentricLoc acentricPower acentricReflection acentric
113.49-44.281.460.10207
17.96-13.491.100919
15.64-7.961.70.102295
14.37-5.641.180.104064
13.57-4.371.240.106411
13.01-3.571.720.109264
12.61-3.012.770.1012577
12.3-2.613.420.1016575
213.49-44.280.9911.50.12206
27.96-13.4917.10.17918
25.64-7.960.975.80.182295
24.37-5.640.995.20.184063
23.57-4.370.994.80.186411
23.01-3.570.994.80.169264
22.61-3.010.985.60.1212577
22.3-2.610.995.80.0916547
313.49-44.280.8936.10.46203
37.96-13.490.8526.40.61913
35.64-7.960.7617.50.832295
34.37-5.640.6610.21.294064
33.57-4.370.617.31.696411
33.01-3.570.696.11.699264
32.61-3.010.876.61.3212577
32.3-2.611.016.71.0616575
413.49-44.280.928.10.47207
47.96-13.490.8520.40.63917
45.64-7.960.7613.50.872295
44.37-5.640.698.41.274064
43.57-4.370.676.71.56411
43.01-3.570.745.71.479264
42.61-3.010.8861.1712577
42.3-2.6116.20.9316575
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1ano20-0.201-0.78-0.9360
2ano20-0.296-0.852-0.9110
3ano20-0.133-0.886-0.9360
4ano20-0.037-0.815-0.9110
5ano20-0.608-0.925-0.8570
6ano20-0.303-0.811-0.9050
7ano20-0.05-0.933-0.990
8ano20-0.725-0.741-0.8570
9ano20-0.028-0.854-0.9050
10ano20-0.256-0.286-0.8580
11ano20-0.284-0.735-0.990
12ano20-0.973-0.779-1.0020
13ano20-0.294-0.297-0.6950
14ano20-0.096-0.769-0.770
15ano20-0.7-0.11-0.8890
16ano20-0.649-0.991-0.9460
17ano20-0.361-0.888-1.0020
18ano20-0.633-0.557-0.890
19ano20-0.591-0.964-0.8440
20ano20-0.826-0.916-0.7380
21ano20-0.039-0.372-0.6950
22ano20-0.742-0.702-0.8430
23ano20-0.681-0.674-0.9450
24ano20-0.237-0.898-0.770
25ano20-0.612-0.938-0.8140
26ano20-0.195-0.782-0.9380.071
27ano20-0.298-0.853-0.910.31
28ano20-0.135-0.882-0.9390.056
29ano20-0.036-0.815-0.9110.31
30ano20-0.607-0.923-0.8570.277
31ano20-0.304-0.814-0.9060.265
32ano20-0.088-1.028-1.04-0.034
33ano20-0.725-0.74-0.8570.265
34ano20-0.028-0.85-0.9060.33
35ano20-0.247-0.259-0.850.064
36ano20-0.272-0.645-0.9820.021
37ano20-0.919-0.701-0.984-0.025
38ano20-0.319-0.32-0.6920.024
39ano20-0.101-0.774-0.7630.109
40ano20-0.706-0.105-0.880.113
41ano20-0.638-0.985-0.9460.069
42ano200.823-0.0020.4690.006
43ano20-0.597-0.544-0.886-0.006
44ano20-0.586-0.956-0.850.094
45ano20-0.826-0.918-0.7350.16
46ano20-0.036-0.368-0.6920.103
47ano20-0.623-0.635-0.852-0.001
48ano20-0.715-0.698-0.9420.116
49ano20-0.233-0.898-0.7650.093
50ano20-0.516-0.925-0.768-0.099
51ano20-0.202-0.779-0.9363.263
52ano20-0.295-0.853-0.9122.75
53ano20-0.131-0.887-0.9363.193
54ano20-0.039-0.814-0.9122.738
55ano20-0.607-0.924-0.8572.727
56ano20-0.303-0.808-0.9052.444
57ano20-0.05-0.931-0.992.41
58ano20-0.726-0.741-0.8572.799
59ano20-0.03-0.858-0.9052.431
60ano20-0.251-0.281-0.8610.227
61ano20-0.284-0.735-0.9912.471
62ano20-0.972-0.779-1.0022.448
63ano20-0.293-0.296-0.6961.474
64ano20-0.095-0.77-0.7711.358
65ano20-0.7-0.11-0.892.086
66ano20-0.652-0.992-0.9462.447
67ano20-0.361-0.888-1.0022.413
68ano20-0.634-0.557-0.892.067
69ano20-0.591-0.966-0.8442.055
70ano20-0.824-0.914-0.7391.663
71ano20-0.04-0.373-0.6961.429
72ano20-0.743-0.7-0.8431.897
73ano20-0.68-0.674-0.9462.204
74ano20-0.238-0.897-0.7711.664
75ano20-0.611-0.936-0.8140.257
76ano20-0.202-0.779-0.9362.649
77ano20-0.295-0.853-0.9122.089
78ano20-0.131-0.887-0.9362.587
79ano20-0.039-0.814-0.9122.084
80ano20-0.607-0.924-0.8572.196
81ano20-0.303-0.809-0.9051.922
82ano20-0.049-0.931-0.991.848
83ano20-0.727-0.742-0.8572.227
84ano20-0.03-0.858-0.9051.919
85ano20-0.249-0.285-0.8610.232
86ano20-0.284-0.736-0.9911.877
87ano20-0.972-0.779-1.0021.864
88ano20-0.294-0.297-0.6961.169
89ano20-0.095-0.77-0.7711.113
90ano20-0.7-0.111-0.8891.713
91ano20-0.652-0.992-0.9461.826
92ano20-0.36-0.887-1.0021.864
93ano20-0.634-0.557-0.891.653
94ano20-0.591-0.966-0.8441.552
95ano20-0.824-0.914-0.7391.277
96ano20-0.04-0.373-0.6961.131
97ano20-0.743-0.7-0.8431.473
98ano20-0.679-0.673-0.9461.673
99ano20-0.239-0.898-0.7711.352
100ano20-0.614-0.937-0.8140.245
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 52312
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.08-10055.80.648522
7.84-10.0853.50.833680
6.64-7.8447.20.879849
5.86-6.6444.90.884966
5.3-5.8640.70.9141138
4.88-5.340.60.9241204
4.54-4.8837.60.931313
4.27-4.54380.9241387
4.04-4.2735.90.9331472
3.84-4.0438.10.9181546
3.67-3.8440.90.8991656
3.52-3.6742.70.8941709
3.39-3.5244.10.8831783
3.27-3.3945.90.8611841
3.16-3.2754.80.7791906
3.07-3.1655.60.7951997
2.98-3.0758.20.7732038
2.9-2.9857.10.7612122
2.82-2.959.10.7532139
2.75-2.8263.70.7292144
2.69-2.75640.7322281
2.63-2.6965.90.722350
2.57-2.6368.30.7062363
2.52-2.5769.90.6982381
2.47-2.52710.6772493
2.42-2.4774.40.6472558
2.38-2.4272.40.6862515
2.3-2.3877.10.6214959

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM4.2phasing
CNS1.1refinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.19 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1856 5 %random
Rwork0.224 ---
all0.226 37534 --
obs0.225 37329 99.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 48.2841 Å2 / ksol: 0.344122 e/Å3
Displacement parametersBiso max: 97.93 Å2 / Biso mean: 44.94 Å2 / Biso min: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å24.93 Å20 Å2
2--4.12 Å20 Å2
3----8.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 0 153 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.2192.5
X-RAY DIFFRACTIONc_scbond_it2.6342
X-RAY DIFFRACTIONc_scangle_it4.0943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.140.2832224.80.27644120.0194685463498.9
2.14-2.260.3062645.70.27143830.0194681464799.3
2.26-2.40.3142194.70.26144150.0214668463499.3
2.4-2.580.2862204.70.24744310.0194681465199.4
2.58-2.840.332324.90.25744580.0224709469099.6
2.84-3.250.3071994.30.24844600.0224690465999.3
3.25-4.10.2382405.10.20744510.0154706469199.7
4.1-29.190.2012605.50.18844630.0124749472399.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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  • 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

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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

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