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- PDB-1gvn: Crystal Structure of the Plasmid Maintenance System epsilon/zeta:... -

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Basic information

Entry
Database: PDB / ID: 1gvn
TitleCrystal Structure of the Plasmid Maintenance System epsilon/zeta: Meachnism of toxin inactivation and toxin function
Components
  • EPSILON
  • ZETA
KeywordsPOSTSEGREGATIONAL KILLING SYSTEM / PLASMID
Function / homology
Function and homology information


UDP-N-acetylglucosamine kinase / negative regulation of cell killing / toxic substance binding / response to toxic substance / kinase activity / ATP binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #130 / Zeta toxin domain / Bacterial epsilon antitoxin / Antitoxin epsilon/PezA domain superfamily / Zeta toxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Helicase, Ruva Protein; domain 3 - #130 / Zeta toxin domain / Bacterial epsilon antitoxin / Antitoxin epsilon/PezA domain superfamily / Zeta toxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Toxin zeta / Antitoxin epsilon
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsMeinhart, A. / Alonso, J.C. / Straeter, N. / Saenger, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of the Plasmid Maintenance System Epsilon /Zeta : Functional Mechanism of Toxin Zeta and Inactivation by Epsilon 2 Zeta 2 Complex Formation
Authors: Meinhart, A. / Alonso, J.C. / Strater, N. / Saenger, W.
History
DepositionFeb 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: EPSILON
B: ZETA
C: EPSILON
D: ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5506
Polymers86,3584
Non-polymers1922
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.236, 79.847, 191.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.19973, 0.76907, 0.60715), (0.7701, -0.50633, 0.38803), (0.60585, 0.39007, -0.69339)-43.39098, 35.16201, 41.26033
2given(0.21431, 0.77442, 0.59526), (0.77824, -0.50366, 0.37506), (0.59027, 0.38288, -0.71063)-43.33834, 35.29405, 42.00922
DetailsTHE TETRAMERIC ASSEMBLY CONSISTS OF 2 HETERO DIMERS OFEPSILON AND ZETA (A,C AND B,D)

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Components

#1: Protein EPSILON


Mass: 10734.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ENCODED ON PLASMID PSM19035 / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / References: UniProt: Q57231
#2: Protein ZETA


Mass: 32444.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ENCODED ON PLASMID PSM19035 / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / References: UniProt: Q54944
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.75 Å3/Da / Density % sol: 48 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Meinhart, A., (2001) Acta Crystallogr., D57, 745.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
35 mMdithiothreitol1drop
4100 mMsodium acetate1reservoirpH4.6
516 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.01629
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01629 Å / Relative weight: 1
ReflectionResolution: 1.95→19.96 Å / Num. obs: 64215 / % possible obs: 95.5 % / Redundancy: 5 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.14 / % possible all: 91.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEV. 1.17phasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3157 5.1 %RANDOM
Rwork0.2 ---
obs0.2 62259 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7859 Å2 / ksol: 0.338413 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20 Å2
2--0.89 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 10 696 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 476 4.9 %
Rwork0.214 9154 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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