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- PDB-6y93: Crystal structure of the DNA-binding domain of the Nucleoid Occlu... -

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Basic information

Entry
Database: PDB / ID: 6y93
TitleCrystal structure of the DNA-binding domain of the Nucleoid Occlusion Factor (Noc) complexed to the Noc-binding site (NBS)
Components
  • Noc Binding Site (NBS)
  • Nucleoid occlusion protein
KeywordsDNA BINDING PROTEIN / chromosome segregation / chromosome maintenance / protein-DNA recognition / evolution / DNA-binding protein
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / nucleoid / division septum assembly / chromosome segregation / chromosome / DNA binding / cytoplasm
Similarity search - Function
Nucleoid occlusion protein / ParB/Spo0J, HTH domain / HTH domain found in ParB protein / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin 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: 2.23 Å
AuthorsJalal, A.S.B. / Tran, N.T. / Stevenson, C.E.M. / Chan, E. / Lo, R. / Tan, X. / Noy, A. / Lawson, D.M. / Le, T.B.K.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Royal SocietyUF140053 United Kingdom
Royal SocietyRG150448 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P018165/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000C0683 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9791 United Kingdom
CitationJournal: Cell Rep / Year: 2020
Title: Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family.
Authors: Jalal, A.S.B. / Tran, N.T. / Stevenson, C.E. / Chan, E.W. / Lo, R. / Tan, X. / Noy, A. / Lawson, D.M. / Le, T.B.K.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Nucleoid occlusion protein
B: Nucleoid occlusion protein
C: Noc Binding Site (NBS)
D: Noc Binding Site (NBS)


Theoretical massNumber of molelcules
Total (without water)47,1164
Polymers47,1164
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-37 kcal/mol
Surface area17730 Å2
Unit cell
Length a, b, c (Å)134.139, 60.567, 81.053
Angle α, β, γ (deg.)90.000, 116.880, 90.000
Int Tables number5
Space group name H-MC121
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
11GLUGLUGLNGLNAA126 - 22717 - 118
21GLUGLUGLNGLNBB126 - 22717 - 118
12DGDGDCDCCC1 - 221 - 22
22DGDGDCDCDD1 - 221 - 22

NCS ensembles :
ID
1
2

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Components

#1: Protein Nucleoid occlusion protein / Noc


Mass: 16806.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The expressed protein comprised residues 111-242 of the wild-type sequence with an additional N-terminal Met residue and a C-terminal nickel affinity tag of sequence KLAAALEHHHHHH from the ...Details: The expressed protein comprised residues 111-242 of the wild-type sequence with an additional N-terminal Met residue and a C-terminal nickel affinity tag of sequence KLAAALEHHHHHH from the pET21b expression plasmid
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: noc, yyaA, BSU40990 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / Variant (production host): Solu / References: UniProt: P37524
#2: DNA chain Noc Binding Site (NBS)


Mass: 6751.378 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chains C and D form a symmetrical DNA duplex which is similar to the Noc Binding Site (NBS) sequence from Bacillus subtilis without 5' phosphates
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: 3.94 Å3/Da / Density % sol: 68.8 %
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.23→72.3 Å / Num. obs: 10830 / % possible obs: 38.1 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.23-2.6611.40.8515420.8470.2580.8914.7
8.57-72.3130.03654110.010.037100

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Processing

Software
NameVersionClassification
STARANISOv3.311 29-Sep-2019data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
DIALS2.1.0data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S6H

6s6h


Resolution: 2.23→72.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU ML: 0.385 / SU R Cruickshank DPI: 0.3856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED This structure was refined after applying an anisotropic correction to the data with STARANISO. In line with the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED This structure was refined after applying an anisotropic correction to the data with STARANISO. In line with the recommendations of the PDB and the STARANISO webpages, the uploaded data cif file contains three data blocks: 1. the STARANISO corrected data that was used to refine the structure, 2. the full uncorrected dataset with no resolution cut-off applied, 3. the output from refmac5 with filled-in data removed to leave only the reflections that were observed within the ellipsoidal resolution cut-off. The latter contains blurred map coefficients that should enable reproduction of the maps that were used to evaluate the model. N.B. The anisotropic correction leads to poor completeness in the higher spherical resolution shells resulting in maps that appear to be at lower resolution than the 2.23 Ang maximum resolution of the corrected data. Since the Rfree and RSRZ scores which evaluate the fit of the model to the data are dependent on the maximum reported resolution, they are inevitably poor for this model. Also note that the map coefficients automatically generated by the deposition process have unfortunately re-instated the above mentioned filled-in reflections. Thus, these will produce maps with an element of model bias i.e. they will tend to reproduce the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 599 5.5 %RANDOM
Rwork0.2313 ---
obs0.2337 10231 38.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 199.06 Å2 / Biso mean: 140.199 Å2 / Biso min: 121.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å20 Å27.99 Å2
2--4.15 Å20 Å2
3----5.05 Å2
Refinement stepCycle: final / Resolution: 2.23→72.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 896 0 0 2591
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122713
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182180
X-RAY DIFFRACTIONr_angle_refined_deg1.0271.4543859
X-RAY DIFFRACTIONr_angle_other_deg1.1711.9015085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4045219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49224.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90315333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8491510
X-RAY DIFFRACTIONr_chiral_restr0.040.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A30470.12
12B30470.12
21C20420.01
22D20420.01
LS refinement shellResolution: 2.233→2.291 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 2 -
Rwork0.572 10 -
all-12 -
obs--0.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.76232.1721-1.51692.2971-0.75745.926-0.06460.17380.1311-0.08960.06120.38370.4131-0.10530.00340.32840.1493-0.0180.2516-0.00590.385934.7992-16.536319.4295
25.98711.92471.96014.11771.40745.4001-0.02380.3291-0.0414-0.32080.1219-0.2615-0.3192-0.0446-0.09810.33990.16310.02580.16960.07910.308221.897514.706214.2024
38.4777-4.7845-0.58323.63440.25971.1144-0.48430.0828-0.00390.45450.28830.11030.0642-0.01590.1960.10910.1442-0.00610.28220.00760.304529.84380.136723.273
47.783-4.3443-0.40123.57610.18621.1261-0.48740.1137-0.09430.45180.3869-0.0169-0.02830.01250.10050.09790.14760.00220.38310.04620.316528.23460.066823.3334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 230
2X-RAY DIFFRACTION2B113 - 228
3X-RAY DIFFRACTION3C1 - 22
4X-RAY DIFFRACTION4D1 - 22

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