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- PDB-6s6h: Crystal structure of the DNA binding domain of the chromosome-par... -

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Basic information

Entry
Database: PDB / ID: 6s6h
TitleCrystal structure of the DNA binding domain of the chromosome-partitioning protein ParB complexed to the centromeric parS site
Components
  • Chromosome-partitioning protein ParB
  • DNA (5'-D(*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*C)-3')
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 / chromosome segregation / chromosome / DNA binding / cytoplasm
Similarity search - Function
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) / Chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesCaulobacter vibrioides NA1000 (bacteria)
Caulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJalal, A.S.B. / Tran, N.T. / Stevenson, C.E.M. / Tan, E.X. / 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 CouncilBB/P018165/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/J/000C0683 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 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
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Jan 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: Chromosome-partitioning protein ParB
B: Chromosome-partitioning protein ParB
C: DNA (5'-D(*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4566
Polymers43,2724
Non-polymers1842
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-37 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.099, 40.717, 94.004
Angle α, β, γ (deg.)90.000, 121.400, 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
11METMETPROPROAA125 - 2491 - 125
21METMETPROPROBB125 - 2491 - 125
12DGDGDCDCCC1 - 201 - 20
22DGDGDCDCDD1 - 201 - 20

NCS ensembles :
ID
1
2

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Components

#1: Protein Chromosome-partitioning protein ParB


Mass: 15502.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The expressed protein comprised residues 126-254 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 126-254 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.) Caulobacter vibrioides NA1000 (bacteria)
Gene: parB, CCNA_03868 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta Solu / References: UniProt: B8GW30
#2: DNA chain DNA (5'-D(*GP*AP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*TP*C)-3')


Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chains C and D form a symmetrical DNA duplex which is similar to the parS sequence from Caulobacter vibrioides without 5' phosphates
Source: (synth.) Caulobacter vibrioides (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→40.12 Å / Num. obs: 16317 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.15 / Net I/σ(I): 7 / Num. measured all: 105021 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1 / % possible all: 99.2

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.4-2.496.60.8011094216620.850.3330.8692
8.98-40.125.80.120823560.9930.0420.10916

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.11.4data scaling
PDB_EXTRACT3.25data extraction
DIALS1.11.4data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UMK

4umk


Resolution: 2.4→40.12 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.942 / SU B: 19.018 / SU ML: 0.21 / SU R Cruickshank DPI: 0.4347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.435 / ESU R Free: 0.243
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 826 5.1 %RANDOM
Rwork0.2161 ---
obs0.2169 15480 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.81 Å2 / Biso mean: 48.259 Å2 / Biso min: 23.22 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å2-1.86 Å2
2--2.82 Å20 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2.4→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 814 12 82 2825
Biso mean--57.81 40.87 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122857
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182357
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.4754034
X-RAY DIFFRACTIONr_angle_other_deg1.1931.8525461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9821.84892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9871516
X-RAY DIFFRACTIONr_chiral_restr0.0440.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A34620.07
12B34620.07
21C17580.01
22D17580.01
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 59 -
Rwork0.318 1096 -
all-1155 -
obs--98.89 %
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)
12.12520.08670.40461.4335-0.45293.0199-0.0528-0.0273-0.3298-0.1148-0.0222-0.02740.25940.15040.0750.03890.0197-0.00250.22610.01070.114516.1413-4.924815.5357
21.4866-0.0623-0.5520.6882-0.6350.92180.0006-0.07510.03410.0455-0.0260.0053-0.1138-0.0920.02540.09310.0251-0.07890.3799-0.01910.0714-18.62756.39418.0931
35.71590.11870.12441.09660.29081.38660.0143-0.4296-0.27150.1872-0.05370.11360.006-0.07360.03950.0338-0.00070.02050.13380.03550.03040.2783-0.086925.2741
46.10180.87920.12850.8941-0.08011.2633-0.0079-0.3138-0.05690.1823-0.0415-0.0337-0.01310.0160.04940.0442-0.0029-0.00650.11370.02280.007-0.32860.242825.2625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 250
2X-RAY DIFFRACTION2B125 - 301
3X-RAY DIFFRACTION3C1 - 20
4X-RAY DIFFRACTION4D1 - 20

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