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- PDB-3nfc: Crystal structure of E.coli MazF Toxin -

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Basic information

Entry
Database: PDB / ID: 3nfc
TitleCrystal structure of E.coli MazF Toxin
ComponentsPemK-like protein 1
KeywordsTOXIN / MazF / MazEF system / RNA cleavage
Function / homology
Function and homology information


toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity ...toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity / negative regulation of cell growth / regulation of translation / defense response to virus / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease toxin MazF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, X. / Wang, K. / Su, X. / Zhang, J.
CitationJournal: To be Published
Title: Biochemical and Structural Analysis of E. coli MazF Toxin
Authors: Wang, X. / Wang, K. / Gao, X. / Zhang, X. / Li, L. / Su, X. / Zhang, J.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PemK-like protein 1
B: PemK-like protein 1
C: PemK-like protein 1
D: PemK-like protein 1
E: PemK-like protein 1
F: PemK-like protein 1


Theoretical massNumber of molelcules
Total (without water)72,6726
Polymers72,6726
Non-polymers00
Water3,819212
1
A: PemK-like protein 1

A: PemK-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area9990 Å2
MethodPISA
2
B: PemK-like protein 1
C: PemK-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area9370 Å2
MethodPISA
3
D: PemK-like protein 1
E: PemK-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-10 kcal/mol
Surface area9640 Å2
MethodPISA
4
F: PemK-like protein 1

F: PemK-like protein 1


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.100, 111.800, 93.000
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRASPASPAA5 - 185 - 18
21TYRTYRPHEPHEBB5 - 175 - 17
31TYRTYRPHEPHECC5 - 175 - 17
41TYRTYRPHEPHEDD5 - 175 - 17
51TYRTYRASPASPEE5 - 185 - 18
61ARGARGPHEPHEFF4 - 174 - 17
12HISHISGLYGLYAA28 - 6628 - 66
22ARGARGGLYGLYBB29 - 6629 - 66
32HISHISGLYGLYCC28 - 6628 - 66
42HISHISGLYGLYDD28 - 6628 - 66
52HISHISGLYGLYEE28 - 6628 - 66
62ARGARGGLYGLYFF29 - 6629 - 66
13GLYGLYGLYGLYAA71 - 11171 - 111
23GLYGLYGLYGLYBB71 - 11171 - 111
33GLYGLYGLYGLYCC71 - 11171 - 111
43GLYGLYGLYGLYDD71 - 11171 - 111
53GLYGLYGLYGLYEE71 - 11171 - 111
63GLYGLYGLYGLYFF71 - 11171 - 111

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PemK-like protein 1 / Protein mazF


Mass: 12112.022 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE70
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris-HCl, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 40587 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB4
Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.286 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29072 2112 5.1 %RANDOM
Rwork0.24898 ---
obs0.251 39622 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.19 Å2 / Biso mean: 43.655 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20.28 Å2
2---0.22 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 0 212 4349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.9815714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22724.242132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0615687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6281518
X-RAY DIFFRACTIONr_chiral_restr0.140.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213045
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.52769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79624447
X-RAY DIFFRACTIONr_scbond_it2.80931438
X-RAY DIFFRACTIONr_scangle_it4.0884.51267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A48TIGHT POSITIONAL0.040.05
12B48TIGHT POSITIONAL0.030.05
13C48TIGHT POSITIONAL0.040.05
14D48TIGHT POSITIONAL0.040.05
15E48TIGHT POSITIONAL0.050.05
16F48TIGHT POSITIONAL0.030.05
11A51MEDIUM POSITIONAL0.040.5
12B51MEDIUM POSITIONAL0.050.5
13C51MEDIUM POSITIONAL0.050.5
14D51MEDIUM POSITIONAL0.050.5
15E51MEDIUM POSITIONAL0.050.5
16F51MEDIUM POSITIONAL0.040.5
11A48TIGHT THERMAL0.110.5
12B48TIGHT THERMAL0.130.5
13C48TIGHT THERMAL0.180.5
14D48TIGHT THERMAL0.160.5
15E48TIGHT THERMAL0.080.5
16F48TIGHT THERMAL0.150.5
11A51MEDIUM THERMAL0.142
12B51MEDIUM THERMAL0.162
13C51MEDIUM THERMAL0.172
14D51MEDIUM THERMAL0.162
15E51MEDIUM THERMAL0.122
16F51MEDIUM THERMAL0.132
21A152TIGHT POSITIONAL0.050.05
22B152TIGHT POSITIONAL0.050.05
23C152TIGHT POSITIONAL0.050.05
24D152TIGHT POSITIONAL0.050.05
25E152TIGHT POSITIONAL0.050.05
26F152TIGHT POSITIONAL0.050.05
21A119MEDIUM POSITIONAL0.060.5
22B119MEDIUM POSITIONAL0.050.5
23C119MEDIUM POSITIONAL0.060.5
24D119MEDIUM POSITIONAL0.060.5
25E119MEDIUM POSITIONAL0.050.5
26F119MEDIUM POSITIONAL0.060.5
21A152TIGHT THERMAL0.130.5
22B152TIGHT THERMAL0.130.5
23C152TIGHT THERMAL0.150.5
24D152TIGHT THERMAL0.150.5
25E152TIGHT THERMAL0.150.5
26F152TIGHT THERMAL0.150.5
21A119MEDIUM THERMAL0.162
22B119MEDIUM THERMAL0.142
23C119MEDIUM THERMAL0.142
24D119MEDIUM THERMAL0.182
25E119MEDIUM THERMAL0.172
26F119MEDIUM THERMAL0.172
31A164TIGHT POSITIONAL0.050.05
32B164TIGHT POSITIONAL0.050.05
33C164TIGHT POSITIONAL0.050.05
34D164TIGHT POSITIONAL0.060.05
35E164TIGHT POSITIONAL0.050.05
36F164TIGHT POSITIONAL0.050.05
31A132MEDIUM POSITIONAL0.060.5
32B132MEDIUM POSITIONAL0.070.5
33C132MEDIUM POSITIONAL0.060.5
34D132MEDIUM POSITIONAL0.060.5
35E132MEDIUM POSITIONAL0.060.5
36F132MEDIUM POSITIONAL0.060.5
31A164TIGHT THERMAL0.130.5
32B164TIGHT THERMAL0.130.5
33C164TIGHT THERMAL0.120.5
34D164TIGHT THERMAL0.150.5
35E164TIGHT THERMAL0.150.5
36F164TIGHT THERMAL0.130.5
31A132MEDIUM THERMAL0.162
32B132MEDIUM THERMAL0.142
33C132MEDIUM THERMAL0.152
34D132MEDIUM THERMAL0.152
35E132MEDIUM THERMAL0.152
36F132MEDIUM THERMAL0.142
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 123 -
Rwork0.425 2262 -
obs--72.85 %
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)
15.5906-1.2168-2.70016.87128.12956.2914-0.17210.36010.12570.87340.0310.57230.9087-0.21530.14110.4133-0.0150.09250.28250.12760.270117.533-5.048-0.555
23.54370.5282-0.51971.825-0.46667.8660.2016-0.2259-0.03290.30560.10550.2290.2135-0.0174-0.3070.40440.05730.12360.18540.08880.204923.4290.4384.166
33.1966-0.0129-0.32973.81080.14213.77550.1586-0.10510.11010.12360.08550.0891-0.0891-0.0676-0.24410.38170.04110.14290.20520.06680.160624.1142.5183.546
42.02191.3689-5.68831.62810.97784.5112-0.3774-0.1169-0.3025-0.03590.3050.3660.67410.36830.07240.35880.0319-0.070.39220.20790.258211.25212.6-16.39
51.5598-0.03440.02673.40280.51277.52630.0964-0.1775-0.19520.26570.2740.0610.06450.0617-0.37040.22720.0224-0.00020.35680.16530.177511.36320.352-11.362
63.3254-0.5653-1.16354.47140.56653.81540.103-0.0561-0.04240.06220.14240.1410.0182-0.0918-0.24550.25560.0508-0.01470.34070.17960.15310.2421.833-12.092
75.72450.00911.74155.8465-4.51767.98070.2373-0.1380.20710.2336-0.3070.0155-0.24811.00780.06970.3122-0.01140.10480.32940.06640.221526.85939.897-14.492
82.13390.9275-0.0341.83450.978412.23240.21170.25890.2576-0.12770.1847-0.19540.05040.1079-0.39650.33350.09860.09220.24790.09510.198620.81235.756-19.708
93.63090.21650.26393.6199-0.25393.56240.13340.0540.2529-0.0520.0990.0226-0.1279-0.099-0.23240.31290.0840.10820.27280.11670.164518.61536.213-18.947
103.68713.0447-1.2882.17773.62989.44160.41370.2831-0.57080.756-0.3150.00970.6725-0.908-0.09870.4911-0.0496-0.25270.3336-0.0350.2744515.53631.724
112.95030.7411-0.39542.06910.03727.3370.18110.189-0.0167-0.14230.19870.1289-0.0659-0.076-0.37980.32750.0771-0.16990.2397-0.08750.168711.28619.71426.774
123.11440.3372-1.22432.771-0.01762.62360.16990.0044-0.1226-0.10460.0897-0.0290.08650.1239-0.25960.32940.0901-0.18410.3096-0.11090.177713.8319.12827.575
132.83143.78882.03276.7170.94745.5882-0.39650.13930.5155-0.08820.27880.0655-0.7272-0.38190.11770.34060.0556-0.0560.3335-0.16870.305119.91942.89130.397
141.49990.15690.00263.0275-0.34458.73320.1114-0.17240.19840.23680.1978-0.094-0.0299-0.0598-0.30920.22980.0097-0.05370.3478-0.17410.170220.51735.0935.037
153.4005-0.29110.34774.2256-0.57093.36920.1481-0.10080.10920.09570.1109-0.21360.03030.2041-0.2590.25370.0637-0.0680.3467-0.20520.149221.96633.67634.411
165.7506-1.6780.7818.6232.70546.61380.24850.49330.0857-0.1625-0.0498-0.6067-0.54980.5142-0.19870.40430.0032-0.17160.2927-0.07360.223817.29158.568-47.665
172.7230.33670.07171.6026-0.40718.24150.2163-0.1017-0.01690.18590.1538-0.1853-0.0676-0.1153-0.37010.36790.0528-0.19050.1988-0.0740.167710.11854.572-42.421
183.3126-0.4656-0.6393.2932-0.50243.85830.0606-0.0683-0.08540.06030.1802-0.10490.2479-0.0027-0.24080.42390.0354-0.24430.2064-0.06040.15719.4952.943-43.087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 18
2X-RAY DIFFRACTION2A28 - 66
3X-RAY DIFFRACTION3A71 - 111
4X-RAY DIFFRACTION4B5 - 17
5X-RAY DIFFRACTION5B29 - 66
6X-RAY DIFFRACTION6B71 - 111
7X-RAY DIFFRACTION7C5 - 17
8X-RAY DIFFRACTION8C28 - 66
9X-RAY DIFFRACTION9C71 - 111
10X-RAY DIFFRACTION10D5 - 17
11X-RAY DIFFRACTION11D28 - 66
12X-RAY DIFFRACTION12D71 - 111
13X-RAY DIFFRACTION13E5 - 18
14X-RAY DIFFRACTION14E28 - 66
15X-RAY DIFFRACTION15E71 - 111
16X-RAY DIFFRACTION16F4 - 17
17X-RAY DIFFRACTION17F29 - 66
18X-RAY DIFFRACTION18F71 - 111

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