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- PDB-5ceg: X-ray structure of toxin/anti-toxin complex from Mesorhizobium op... -

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Basic information

Entry
Database: PDB / ID: 5ceg
TitleX-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum
Components
  • Addiction module antidote protein, CopG/Arc/MetJ family
  • Plasmid stabilization system
KeywordsTOXIN / Toxin Anti-toxin
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix ...Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Plasmid stabilization system / Addiction module antidote protein, CopG/Arc/MetJ family
Similarity search - Component
Biological speciesMesorhizobium opportunistum
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsAakre, C.D. / Herrou, J. / Crosson, S. / Laub, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2015
Title: Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates.
Authors: Aakre, C.D. / Herrou, J. / Phung, T.N. / Perchuk, B.S. / Crosson, S. / Laub, M.T.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Addiction module antidote protein, CopG/Arc/MetJ family
B: Plasmid stabilization system
C: Addiction module antidote protein, CopG/Arc/MetJ family
D: Plasmid stabilization system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89620
Polymers48,2134
Non-polymers1,68316
Water8,701483
1
A: Addiction module antidote protein, CopG/Arc/MetJ family
B: Plasmid stabilization system
C: Addiction module antidote protein, CopG/Arc/MetJ family
D: Plasmid stabilization system
hetero molecules

A: Addiction module antidote protein, CopG/Arc/MetJ family
B: Plasmid stabilization system
C: Addiction module antidote protein, CopG/Arc/MetJ family
D: Plasmid stabilization system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,79140
Polymers96,4258
Non-polymers3,36632
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area35260 Å2
ΔGint-159 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.180, 118.840, 211.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21A-291-

HOH

31A-301-

HOH

41C-239-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Addiction module antidote protein, CopG/Arc/MetJ family


Mass: 10616.017 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075) (bacteria)
Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5599 / Plasmid: pETDuet-1 / Details (production host): AmpR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: F7YBW8
#2: Protein Plasmid stabilization system


Mass: 13490.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His tagged protein
Source: (gene. exp.) Mesorhizobium opportunistum (strain LMG 24607 / HAMBI 3007 / WSM2075) (bacteria)
Strain: LMG 24607 / HAMBI 3007 / WSM2075 / Gene: Mesop_5598 / Plasmid: pETDuet-1 / Details (production host): AmpR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: F7YBW7

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Non-polymers , 4 types, 499 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.81 Å3/Da / Density % sol: 56.27 % / Description: spear-like crystals
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 400 mM Sodium Acetate, 100 mM Sodium Citrate pH5.5, 20% PEG 4000, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.59→31.3 Å / Num. obs: 73683 / % possible obs: 99.95 % / Redundancy: 9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.5
Reflection shellResolution: 1.59→1.63 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia20.3.6.3data reduction
xia20.3.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.59→29.71 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 1937 2.7 %
Rwork0.1685 --
obs0.1692 73683 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 51 483 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073259
X-RAY DIFFRACTIONf_angle_d1.0684433
X-RAY DIFFRACTIONf_dihedral_angle_d12.0471297
X-RAY DIFFRACTIONf_chiral_restr0.046488
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.61010.32121390.25125064X-RAY DIFFRACTION100
1.6101-1.63130.26741380.23965058X-RAY DIFFRACTION100
1.6313-1.65370.22941440.2285148X-RAY DIFFRACTION100
1.6537-1.67730.22931360.21855061X-RAY DIFFRACTION100
1.6773-1.70230.28741420.21985065X-RAY DIFFRACTION100
1.7023-1.72890.23311470.21895136X-RAY DIFFRACTION100
1.7289-1.75730.29171350.20895077X-RAY DIFFRACTION100
1.7573-1.78760.2761440.20385108X-RAY DIFFRACTION100
1.7876-1.82010.2011420.20385028X-RAY DIFFRACTION100
1.8201-1.85510.2641390.19635105X-RAY DIFFRACTION100
1.8551-1.89290.1951430.19175139X-RAY DIFFRACTION100
1.8929-1.93410.20431380.18345038X-RAY DIFFRACTION100
1.9341-1.97910.19641430.17895117X-RAY DIFFRACTION100
1.9791-2.02850.18431390.16845034X-RAY DIFFRACTION100
2.0285-2.08340.19991460.16255131X-RAY DIFFRACTION100
2.0834-2.14470.20881440.15935044X-RAY DIFFRACTION100
2.1447-2.21390.17881390.15875057X-RAY DIFFRACTION100
2.2139-2.2930.191350.16585117X-RAY DIFFRACTION100
2.293-2.38470.20521450.15815098X-RAY DIFFRACTION100
2.3847-2.49320.19011420.16245018X-RAY DIFFRACTION100
2.4932-2.62460.16931430.16625111X-RAY DIFFRACTION100
2.6246-2.78890.23571410.17615059X-RAY DIFFRACTION100
2.7889-3.00410.20221400.16755105X-RAY DIFFRACTION100
3.0041-3.3060.16241460.1545078X-RAY DIFFRACTION100
3.306-3.78360.14011410.14755053X-RAY DIFFRACTION100
3.7836-4.76370.16551410.13045118X-RAY DIFFRACTION100
4.7637-29.71520.20691370.17165071X-RAY DIFFRACTION100

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