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- PDB-7bm8: Crystal structure of the C-terminally truncated chromosome-partit... -

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Basic information

Entry
Database: PDB / ID: 7bm8
TitleCrystal structure of the C-terminally truncated chromosome-partitioning protein ParB from Caulobacter crescentus complexed with CTP-gamma-S
ComponentsChromosome-partitioning protein ParB
KeywordsDNA BINDING PROTEIN / chromosome segregation / CTP / molecular gates / protein-DNA recognition
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
CYTIDINE-5'-TRIPHOSPHATE / Chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsJalal, A.S. / Tran, N.T. / Stevenson, C.E.M. / Lawson, D.M. / Le, T.B.K.
Funding support United Kingdom, 4items
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/000PR9791 United Kingdom
CitationJournal: Elife / Year: 2021
Title: A CTP-dependent gating mechanism enables ParB spreading on DNA.
Authors: Jalal, A.S. / Tran, N.T. / Stevenson, C.E. / Chimthanawala, A. / Badrinarayanan, A. / Lawson, D.M. / Le, T.B.
History
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0656
Polymers56,0502
Non-polymers1,0154
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-50 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.461, 56.076, 71.360
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 42 - 221 / Label seq-ID: 32 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Chromosome-partitioning protein ParB


Mass: 28024.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The expressed protein comprised residues 11-244 of the wild-type sequence with a C-terminal nickel affinity tag of sequence KLAAALEHHHHHH from the pET21b expression plasmid
Source: (gene. exp.) Caulobacter vibrioides (strain NA1000 / CB15N) (bacteria)
Strain: NA1000 / CB15N / Gene: parB, CCNA_03868 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / Variant (production host): Solu / References: UniProt: B8GW30
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.73→70.59 Å / Num. obs: 14516 / % possible obs: 98.8 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.083 / Rrim(I) all: 0.212 / Net I/σ(I): 5.4 / Num. measured all: 92266 / Scaling rejects: 77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.73-2.864.81.21847317560.8250.5991.3571.291.4
9.05-70.595.90.06325614320.9910.0280.06913.599.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T1F

6t1f


Resolution: 2.73→68.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.471 / SU ML: 0.384 / SU R Cruickshank DPI: 0.6609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.661 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The density did not allow the unambiguous placement of the gamma-S of CTP-gamma-S. Thus CTP was refined in its place.
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 678 4.7 %RANDOM
Rwork0.2477 ---
obs0.2493 13824 98.65 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 186.77 Å2 / Biso mean: 68.899 Å2 / Biso min: 33.59 Å2
Baniso -1Baniso -2Baniso -3
1--6.79 Å20 Å21.2 Å2
2---6.21 Å20 Å2
3---12.12 Å2
Refinement stepCycle: final / Resolution: 2.73→68.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 60 0 2716
Biso mean--60.63 --
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132756
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172521
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.6513743
X-RAY DIFFRACTIONr_angle_other_deg1.1051.5775807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.97321.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4031530
X-RAY DIFFRACTIONr_chiral_restr0.0330.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
Refine LS restraints NCS

Ens-ID: 1 / Number: 5284 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.73→2.8 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.405 61 -
Rwork0.371 870 -
obs--84.95 %

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