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- PDB-7ol9: Crystal structure of C-terminally truncated Bacillus subtilis nuc... -

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Basic information

Entry
Database: PDB / ID: 7ol9
TitleCrystal structure of C-terminally truncated Bacillus subtilis nucleoid occlusion protein (Noc) complexed to the Noc-binding site (NBS)
Components
  • DNA (5'-D(*TP*AP*TP*TP*TP*CP*CP*CP*GP*GP*GP*AP*AP*AP*TP*A)-3')
  • Nucleoid occlusion protein
KeywordsDNA BINDING PROTEIN / chromosome segregation / chromosome maintenance / protein-DNA recognition / DNA-binding protein
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / division septum assembly / nucleoid / chromosome segregation / chromosome / DNA binding / cytoplasm
Similarity search - Function
Nucleoid occlusion protein / ParB/Spo0J, HTH domain / ParB HTH domain / : / ParB/RepB/Spo0J partition protein / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleoid occlusion protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJalal, A.S.B. / Lawson, D.M. / Le, T.B.K.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Royal SocietyURF-R-201020 United Kingdom
Wellcome Trust209500 United Kingdom
Royal SocietyRG150448 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS-E-J-000C0683 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc-DNA complex.
Authors: Sukhoverkov, K.V. / Jalal, A.S.B. / Ault, J.R. / Sobott, F. / Lawson, D.M. / Le, T.B.K.
#1: Journal: Biorxiv / Year: 2022
Title: The CTP-binding domain is disengaged from the DNA-binding domain in a co-crystal structure of Bacillus subtilis Noc-DNA complex
Authors: Sukhoverkov, K.V. / Jalal, A.S.B. / Lawson, D.M. / Le, T.B.K.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Nucleoid occlusion protein
B: Nucleoid occlusion protein
C: DNA (5'-D(*TP*AP*TP*TP*TP*CP*CP*CP*GP*GP*GP*AP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*AP*TP*TP*TP*CP*CP*CP*GP*GP*GP*AP*AP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)68,9364
Polymers68,9364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-42 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.501, 99.326, 99.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLNGLNAA30 - 22930 - 229
21ILEILEGLNGLNBB30 - 22930 - 229
12DTDTDADACC1 - 161 - 16
22DTDTDADADD1 - 161 - 16

NCS ensembles :
ID
1
2

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Components

#1: Protein Nucleoid occlusion protein / Noc


Mass: 29570.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The expressed protein corresponds to residues 1-242 of UniProtKB - P37524. The C-terminal sequence KLAAALEHHHHHH is a nickel affinity tag from the pET21b expression plasmid.
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: noc, yyaA, BSU40990 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37524
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*TP*CP*CP*CP*GP*GP*GP*AP*AP*AP*TP*A)-3')


Mass: 4897.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Null

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.89→70.36 Å / Num. obs: 16242 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.118 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.89-3.0713.72.69325780.6840.7522.797
8.67-70.3611.10.03768610.0120.039

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y93

6y93


Resolution: 2.9→70.36 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.934 / SU B: 20.896 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 829 5.2 %RANDOM
Rwork0.2296 ---
obs0.2322 15216 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.63 Å2 / Biso mean: 109.446 Å2 / Biso min: 65.79 Å2
Baniso -1Baniso -2Baniso -3
1-6.73 Å2-0 Å20 Å2
2---1.09 Å2-0 Å2
3----5.64 Å2
Refinement stepCycle: final / Resolution: 2.9→70.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 650 0 0 3843
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123965
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183579
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.555509
X-RAY DIFFRACTIONr_angle_other_deg1.1391.7218251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2055402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99422.686175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77515613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0651526
X-RAY DIFFRACTIONr_chiral_restr0.0470.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02833
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56600.14
12B56600.14
21C13610.06
22D13610.06
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 66 -
Rwork0.407 1101 -
all-1167 -
obs--100 %

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