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- PDB-6iya: Structure of the DNA binding domain of antitoxin CopASO -

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Basic information

Entry
Database: PDB / ID: 6iya
TitleStructure of the DNA binding domain of antitoxin CopASO
ComponentsTranscriptional regulator CopG family
KeywordsANTITOXIN / RHH / DNA binding
Function / homologyRibbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Transcriptional regulator CopG family
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsZhao, R. / Li, F. / Liu, L. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470775 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structure and allosteric coupling of type II antitoxin CopASO.
Authors: Zhao, R. / Li, Q. / Zhang, J. / Li, F. / Yao, J. / Zhang, J. / Liu, L. / Wang, X. / Zhang, X.
History
DepositionDec 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator CopG family
B: Transcriptional regulator CopG family
C: Transcriptional regulator CopG family
D: Transcriptional regulator CopG family
E: Transcriptional regulator CopG family
F: Transcriptional regulator CopG family


Theoretical massNumber of molelcules
Total (without water)47,9656
Polymers47,9656
Non-polymers00
Water30617
1
A: Transcriptional regulator CopG family
B: Transcriptional regulator CopG family


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-25 kcal/mol
Surface area6220 Å2
MethodPISA
2
C: Transcriptional regulator CopG family
D: Transcriptional regulator CopG family


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-21 kcal/mol
Surface area6130 Å2
MethodPISA
3
E: Transcriptional regulator CopG family

E: Transcriptional regulator CopG family


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3570 Å2
ΔGint-23 kcal/mol
Surface area6370 Å2
MethodPISA
4
F: Transcriptional regulator CopG family

F: Transcriptional regulator CopG family


Theoretical massNumber of molelcules
Total (without water)15,9882
Polymers15,9882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3760 Å2
ΔGint-23 kcal/mol
Surface area6590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.541, 60.949, 105.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 20 or resid 22...
21(chain B and (resid 5 through 20 or resid 22...
31(chain C and (resid 5 through 20 or resid 22...
41(chain D and (resid 5 through 20 or resid 22...
51(chain E and (resid 5 through 20 or resid 22...
61(chain F and (resid 5 through 20 or resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 20 or resid 22...A5 - 20
121(chain A and (resid 5 through 20 or resid 22...A22 - 27
131(chain A and (resid 5 through 20 or resid 22...A2 - 49
141(chain A and (resid 5 through 20 or resid 22...A0
151(chain A and (resid 5 through 20 or resid 22...A40 - 49
211(chain B and (resid 5 through 20 or resid 22...B5 - 20
221(chain B and (resid 5 through 20 or resid 22...B22 - 27
231(chain B and (resid 5 through 20 or resid 22...B30 - 35
241(chain B and (resid 5 through 20 or resid 22...B37 - 38
251(chain B and (resid 5 through 20 or resid 22...B40 - 49
311(chain C and (resid 5 through 20 or resid 22...C5 - 20
321(chain C and (resid 5 through 20 or resid 22...C22 - 27
331(chain C and (resid 5 through 20 or resid 22...C5 - 49
341(chain C and (resid 5 through 20 or resid 22...C0
351(chain C and (resid 5 through 20 or resid 22...C40 - 49
411(chain D and (resid 5 through 20 or resid 22...D5 - 20
421(chain D and (resid 5 through 20 or resid 22...D22 - 27
431(chain D and (resid 5 through 20 or resid 22...D30 - 35
441(chain D and (resid 5 through 20 or resid 22...D37 - 38
451(chain D and (resid 5 through 20 or resid 22...D40 - 49
511(chain E and (resid 5 through 20 or resid 22...E5 - 20
521(chain E and (resid 5 through 20 or resid 22...E22 - 27
531(chain E and (resid 5 through 20 or resid 22...E30 - 35
541(chain E and (resid 5 through 20 or resid 22...E37 - 38
551(chain E and (resid 5 through 20 or resid 22...E40 - 49
611(chain F and (resid 5 through 20 or resid 22...F5 - 20
621(chain F and (resid 5 through 20 or resid 22...F22 - 27
631(chain F and (resid 5 through 20 or resid 22...F30 - 35
641(chain F and (resid 5 through 20 or resid 22...F37 - 38
651(chain F and (resid 5 through 20 or resid 22...F40 - 49

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Components

#1: Protein
Transcriptional regulator CopG family / CopASO


Mass: 7994.143 Da / Num. of mol.: 6 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1445 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGZ2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium formate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7302 / % possible obs: 90.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 48.68 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.042 / Rrim(I) all: 0.098 / Χ2: 0.911 / Net I/σ(I): 15.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 729 / CC1/2: 0.949 / Rpim(I) all: 0.378 / Rrim(I) all: 0.873 / Χ2: 0.852 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GPE

2gpe


Resolution: 3→42.22 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.54
RfactorNum. reflection% reflection
Rfree0.2981 338 4.9 %
Rwork0.2469 --
obs0.2493 6895 86.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.15 Å2 / Biso mean: 50.6612 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 3→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 0 17 2431
Biso mean---35.41 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022498
X-RAY DIFFRACTIONf_angle_d0.5833336
X-RAY DIFFRACTIONf_chiral_restr0.072357
X-RAY DIFFRACTIONf_plane_restr0.004426
X-RAY DIFFRACTIONf_dihedral_angle_d22.4581032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION23.673TORSIONAL
12B1194X-RAY DIFFRACTION23.673TORSIONAL
13C1194X-RAY DIFFRACTION23.673TORSIONAL
14D1194X-RAY DIFFRACTION23.673TORSIONAL
15E1194X-RAY DIFFRACTION23.673TORSIONAL
16F1194X-RAY DIFFRACTION23.673TORSIONAL
LS refinement shellResolution: 3→3.7795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2866 161 -
Rwork0.2599 3126 -
obs--85 %
Refinement TLS params.Method: refined / Origin x: 18.8911 Å / Origin y: -17.0802 Å / Origin z: -17.1784 Å
111213212223313233
T0.1786 Å2-0.0111 Å20.0219 Å2-0.2744 Å2-0.032 Å2--0.2573 Å2
L2.1834 °2-1.17 °21.677 °2-2.365 °2-1.1837 °2--3.3375 °2
S0.102 Å °0.1618 Å °0.0812 Å °0.0814 Å °-0.2086 Å °0.1497 Å °0.0491 Å °0.1244 Å °0.0959 Å °
Refinement TLS groupSelection details: all

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